1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Kowalik M, Masternak J, Olszewski M, Maciejewska N, Kazimierczuk K, Sitkowski J, Dąbrowska AM, Chylewska A, Makowski M. Anticancer Study on Ir III and Rh III Half-Sandwich Complexes with the Bipyridylsulfonamide Ligand. Inorg Chem 2024; 63:1296-1316. [PMID: 38174357 DOI: 10.1021/acs.inorgchem.3c03801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Organometallic half-sandwich complexes [(η5-Cp)IrCl(L)]PF6 (1) and [(η5-Cp)RhCl(L)]PF6 (2) were prepared using pentamethylcyclopentadienyl chloride dimers of iridium(III) or rhodium(III) with the 4-amino-N-(2,2'-bipyridin-5-yl)benzenesulfonamide ligand (L) and ammonium hexafluorophosphate. The crystal structures of L, 1, and 2 were analyzed in detail. The coordination reactions of the ligand with the central ions were confirmed using various spectroscopic techniques. Additionally, the interactions between sulfaligand, Ir(III), and Rh(III) complexes with carbonic anhydrase (CA), human serum albumin (HSA), and CT-DNA were investigated. The iridium(III) complex (1) did not show any antiproliferative properties against four different cancer cell lines, i.e., nonsmall cell lung cancer A549, colon cancer HCT-116, breast cancer MCF7, lymphoblastic leukemia Nalm-6, and a nonmalignant human embryonic kidney cell line HEK293, due to high binding affinity to GSH. The sulfonamide ligand (L) and rhodium(III) complex (2) were further studied. L showed competitive inhibition toward CA, while complexes 1 and 2, uncompetitive. All compounds interacted with HSA, causing a conformational change in the protein's α-helical structure, suggesting the induction of a more open conformation in HSA, reducing its biological activity. Both L and 2 were found to induce cell death through a caspase-dependent pathway. These findings position L and 2 as potential starting compounds for pharmaceutical, therapeutic, or medicinal research.
Collapse
Affiliation(s)
- Mateusz Kowalik
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Joanna Masternak
- Institute of Chemistry, Jan Kochanowski University in Kielce, Uniwersytecka 7, 25-406 Kielce, Poland
| | - Mateusz Olszewski
- Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Natalia Maciejewska
- Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Katarzyna Kazimierczuk
- Faculty of Chemistry, Gdańsk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Jerzy Sitkowski
- Institute of Organic Chemistry, Polish Academic of Science, Marcina Kasprzaka 44/52, 01-224 Warszawa, Poland
- National Medicines Institute, Chełmska 30/34, 00-725 Warszawa, Poland
| | | | - Agnieszka Chylewska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| |
Collapse
|
3
|
Thomas OE, Oduwole RT, Akin-Taylor A. Comparison of the DNA-binding interactions of 5-hydroxymethylfurfural and its synthesized derivative, 5, 5’[oxy-bis(methylene)]bis-2-furfural: experimental, DFT and docking studies. JOURNAL OF TAIBAH UNIVERSITY FOR SCIENCE 2023. [DOI: 10.1080/16583655.2023.2183705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
|
4
|
Paul P, Sarkar S, Dastidar DG, Shukla A, Das S, Chatterjee S, Chakraborty P, Tribedi P. 1, 4-naphthoquinone efficiently facilitates the disintegration of pre-existing biofilm of Staphylococcus aureus through eDNA intercalation. Folia Microbiol (Praha) 2023; 68:843-854. [PMID: 37142893 DOI: 10.1007/s12223-023-01053-z] [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: 09/30/2022] [Accepted: 04/04/2023] [Indexed: 05/06/2023]
Abstract
1, 4-naphthoquinone, a plant-based quinone derivative, has gained much attention for its effectiveness against several biofilm-linked diseases. The biofilm inhibitory effect of 1, 4-naphthoquinone against Staphylococcus aureus has already been reported in our previous study. We observed that the extracellular DNA (eDNA) could play an important role in holding the structural integrity of the biofilm. Hence, in this study, efforts have been directed to examine the possible interactions between 1, 4-naphthoquinone and DNA. An in silico analysis indicated that 1, 4-naphthoquinone could interact with DNA through intercalation. To validate the same, UV-Vis spectrophotometric analysis was performed in which a hypochromic shift was observed when the said molecule was titrated with calf-thymus DNA (CT-DNA). Thermal denaturation studies revealed a change of 8℃ in the melting temperature (Tm) of CT-DNA when complexed with 1, 4-naphthoquinone. The isothermal calorimetric titration (ITC) assay revealed a spontaneous intercalation between CT-DNA and 1, 4-naphthoquinone with a binding constant of 0.95 ± 0.12 × 108. Furthermore, DNA was run through an agarose gel electrophoresis with a fixed concentration of ethidium bromide and increasing concentrations of 1, 4-naphthoquinone. The result showed that the intensity of ethidium bromide-stained DNA got reduced concomitantly with the gradual increase of 1, 4-naphthoquinone suggesting its intercalating nature. To gain further confidence, the pre-existing biofilm was challenged with ethidium bromide wherein we observed that it could also show biofilm disintegration. Therefore, the results suggested that 1, 4-naphthoquinone could exhibit disintegration of the pre-existing biofilm of Staphylococcus aureus through eDNA intercalation.
Collapse
Affiliation(s)
- Payel Paul
- Microbial Ecology Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India
| | - Sarita Sarkar
- Microbial Ecology Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India
| | - Debabrata Ghosh Dastidar
- Guru Nanak Institute of Pharmaceutical Science and Technology, 157/F Nilgunj Road, Panihati, Kolkata, West Bengal, 700114, India
| | - Aditya Shukla
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Sharmistha Das
- Microbial Ecology Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India
| | - Sudipta Chatterjee
- Microbial Ecology Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India
| | - Poulomi Chakraborty
- Microbial Ecology Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India
| | - Prosun Tribedi
- Microbial Ecology Laboratory, Department of Biotechnology, The Neotia University, Sarisha, West Bengal, 743368, India.
| |
Collapse
|
5
|
Li X, Wu Y, Zhang X, Liu J, Zhang Y, Yuan L, Liu M. Thermodynamic and cellular studies of doxorubicin/daunorubicin loaded by a DNA tetrahedron for diagnostic imaging, chemotherapy, and gene therapy. Int J Biol Macromol 2023; 251:126245. [PMID: 37562474 DOI: 10.1016/j.ijbiomac.2023.126245] [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: 06/02/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
The combined diagnostic imaging, chemotherapy, and gene therapy based on DNA nanocarriers can reduce the toxic side effects and overcome multidrug resistance (MDR). In this study, we designed an antisense oligonucleotides (ASOs)-linked DNA tetrahedron (ASOs-TD). The detection limit of ASOs-TD for MDR1 mRNA was 0.05 μM. By using fluorescence spectroscopy and isothermal titration calorimetry (ITC), the interactions between doxorubicin (DOX) /daunorubicin (DAU) and ASOs-TD were investigated. The number of binding sites (n), binding constant (Ka), entropy change (ΔSo), enthalpy change (ΔHo) and Gibbs free energy change (ΔGo) were obtained. The intercalation of DOX/DAU with ASOs-TD was demonstrated by differential scanning calorimetry (DSC) and quenching researches of potassium ferricyanide K4[Fe(CN)6]. The in vitro release rate of DOX/DAU loaded in ASOs-TD was accelerated by deoxyribonuclease I (DNase I). In vitro cytotoxicity proved the good gene therapy effect of ASOs-TD and the increased cytotoxicity of DOX/DAU to MCF-7/ADR cells. The results of confocal laser scanning microscope (CLSM) suggested that ASOs-TD could effectively identify drug-resistant cells due to its good imaging ability for MDR1 mRNA. This work offers theoretical significance for overcoming MDR using DNA nanostructures which combine diagnostic imaging, chemotherapy, and gene therapy.
Collapse
Affiliation(s)
- Xinyu Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yushu Wu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Xinpeng Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Jie Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Yanqing Zhang
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Lixia Yuan
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China
| | - Min Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China; Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| |
Collapse
|
6
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
7
|
Rahaman A, Anjum F, Kumari A, Shafie A, Alee M, Badr O, Khan SH, Ashour AA, Hazazi A, Arif S, Zeng XA. Deciphering the binding mechanism of an anti-cancer phytochemical plumbagin with calf thymus DNA using biophysical and in silico techniques. Front Chem 2023; 11:1248458. [PMID: 37705997 PMCID: PMC10497110 DOI: 10.3389/fchem.2023.1248458] [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: 06/27/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
Plumbagin (PLM), a plant derivative, is well known for a wide range of therapeutic effects in humans including anti-cancer, anti-inflammatory, anti-oxidant, and anti-microbial. Cytotoxic and genotoxic potential of this phytochemical has been studied which demands further insight. DNA being a major target for several drugs was taken to study against PLM to understand its effects on the cellular system. UV-Vis spectroscopy has indicated the binding of PLM to ctDNA and dye displacement assays have confirmed the formation of PLM-ctDNA complex. The insignificant changes in circular dichroism spectra suggested that PLM is not affecting the structural makeup of the ctDNA, hence the binding could be peripheral and not intercalating. Further, the relative viscosity and minimal change in melting temperature upon the complex formation supported this finding and confirmed the groove binding of PLM. Molecular docking analysis and simulation studies also show PLM as a minor groove binder to DNA and provide details on the interaction dynamics of PLM-DNA complex. Docking followed by a 100 ns simulation reveals the negative Gibbs free energy change (∆G = -6.6 kcal mol-1), and the formation of a stable complex. The PLM- DNA complex with stable dynamics was further supported by different parameters including RMSD, RMSF, SASA, Rg, and the energy profile of interaction. This study provides an insight into the cytotoxic and genotoxic mechanism of PLM which can be a crucial step forward to exploit its therapeutic potential against several diseases including cancer.
Collapse
Affiliation(s)
- Abdul Rahaman
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, Guangdong, China
- School of Food Science and Engineering, Foshan University, Foshan, China
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Aknita Kumari
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mahafooj Alee
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Omnia Badr
- Department of Genetics and Genetic Engineering, Faculty of Agriculture, Benha University, Qalyubia, Egypt
| | - Shaheer Hasan Khan
- Enzymology and Nanotechnology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Sultan Arif
- Department of Plastic Surgery and Burn Unit, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Xin-An Zeng
- Guangdong Key Laboratory of Food Intelligent Manufacturing, Foshan University, Foshan, Guangdong, China
- School of Food Science and Engineering, Foshan University, Foshan, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Overseas Expertise Introduction Centre for Discipline Innovation of Food Nutrition and Human Health (111 Centre), Guangzhou, China
| |
Collapse
|
8
|
Hadidi S, Varmira K, Soltani L. Evaluation of DNA damage induced by acesulfame potassium: spectroscopic, molecular modeling simulations and toxicity studies. J Biomol Struct Dyn 2023; 41:6262-6271. [PMID: 35916031 DOI: 10.1080/07391102.2022.2105955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 10/16/2022]
Abstract
Acesulfame potassium (Ace-K) is a widely used artificial sweetener that has been reported to interact with DNA and cause important genetic damage. However, the type of interaction mechanism is unknown. This study provides an approach to understanding the in vitro mechanism of Ace-K interaction with Ct-DNA using spectroscopic methods combined with molecular simulations. The hypochromic effect as obtained from UV-Vis spectra indicated the formation of the DNA-Ace-K complex in the minor groove. Further evidence for groove binding mode comes from the decrease in Hoechst-DNA fluorescence caused by increasing Ace-K concentrations, alongside no detectable change in MB-DNA emission band intensity. A negative value of ΔH and ΔS represents the hydrogen bonds and van der Waals forces between Ace-K and DNA. Based on the molecular docking, Ace-K was located between the guanine10 and 16 in DNA minor groove and stabilized by two hydrogen bonds and one π-Sulfur interaction. In vitro cell culture results showed that about 5 mg/mL of Ace-K caused the death of 85% of HUVEC cells after 48 h. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Kambiz Varmira
- Research Center of Oils and Fats, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Leila Soltani
- Department of Animal Sciences, College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran
| |
Collapse
|
9
|
Shahabadi N, Abdoli Z, Mardani Z, Hadidi S, Shiri F, Soltani L. DNA interaction studies of a cobalt(III) complex containing β-amino alcohol ligand by spectroscopic and molecular docking methods. J Biomol Struct Dyn 2023; 41:12545-12551. [PMID: 36650998 DOI: 10.1080/07391102.2023.2166994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
In the present research, the feasibility of a Cobalt(III) complex containing β-amino alcohol ligands for affinity with the target calf thymus DNA is demonstrated. In the title complex, [Co(C11H15N2O2)2]Cl, the Co(III) atom is six-coordinated with four N atoms and two O atoms from (2-[(E)-({2-[(2-Hydroxyethyl) amino]ethyl}imino)methyl]phenol) ligand (L). To investigate the molecular interaction between the synthesized complex and DNA, some multi-spectroscopic approaches associated with molecular docking were employed in the physiological buffer (pH 7.4). The results indicated that the Co(III) complex proved to be a minor groove binder with a preference for the A-T region, which was substantiated by displacement studies with Hoechst33258 and Methylene blue (MB) as minor groove binder and intercalator. In addition, the results of the molecular docking study revealed that the Co(III) complex approached the gap between the DNA minor grooves near the spot where the Hoechst was. Furthermore, the results of the cytotoxicity and apoptosis tests for the MCF-7 cell line were also indicative of the positive effects of the complex on controlling the growth and viability of breast cancer.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Abdoli
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Leila Soltani
- Department of Animal Sciences, College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran
| |
Collapse
|
10
|
Amemiya K, Hirotsu Y, Mochizuki H, Higuchi R, Nakagomi T, Goto T, Oyama T, Kondo T, Omata M. Deep targeted sequencing of cytological tumor cells using whole genome amplification. Cancer Cytopathol 2023; 131:58-68. [PMID: 36219530 DOI: 10.1002/cncy.22653] [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: 07/06/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND Genomic profiling in lung cancer is essential for precision medicine. Cytological specimens provide an alternative to formalin-fixed paraffin-embedded (FFPE) samples for comprehensive genomic analysis. However, this approach remains challenging when a limited number of tumor cells are available. We applied whole genome amplification (WGA) to cytology specimens to overcome this limitation. METHODS Using a lung cancer panel targeting 58 genes, we performed next-generation sequencing of whole genome-amplified DNA extracted from cytological specimens containing 10-20 tumor cells (cyto-WGA) and DNA from corresponding FFPE tumor tissue. We compared sequencing data from cyto-WGA and FFPE samples to examine the detection accuracy of copy number variations and oncogenic and drug-matched variants. RESULTS The DNA quality and quantity from cyto-WGA were higher than those from FFPE samples (p < .0005 and p < .05, respectively). Sequencing metrics of cyto-WGA and FFPE tissues showed no difference in the number of mapped reads and mean coverage depth, but there were significant differences in the on-target rate (p < .05) and uniformity (p < .0005). Copy number variations in cyto-WGA samples (n = 211) were higher than in FFPE samples (n = 9) (p < .0001). Fourty nine oncogenic variants were detected in cyto-WGA and 39 in FFPE. Of these variants, 34 (63%) were present in both samples. In addition, all 16 drug-matched variants were detected in FFPE and cyto-WGA samples with 100% concordance. CONCLUSION Cyto-WGA can be a feasible and alternative method to detect oncogenic and drug-matched variants.
Collapse
Affiliation(s)
- Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.,Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.,Department of Pathology, School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Rumi Higuchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Takahiro Nakagomi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Taichiro Goto
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Toshio Oyama
- Pathology Division, Laboratory Department, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Tetsuo Kondo
- Department of Pathology, School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.,The University of Tokyo, Tokyo, Japan
| |
Collapse
|
11
|
Elucidation of binding interactions and mechanism of rivastigmine tartrate with dsDNA via multi-spectroscopic, electrochemical, and molecular docking studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
12
|
Ponkarpagam S, Vennila KN, Elango KP. Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121351. [PMID: 35567820 DOI: 10.1016/j.saa.2022.121351] [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: 03/30/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and 1H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in 1H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.
Collapse
Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624302, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624302, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624302, India.
| |
Collapse
|
13
|
Priyadharshini RD, Ponkarpagam S, Vennila KN, Elango KP. Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121363. [PMID: 35580462 DOI: 10.1016/j.saa.2022.121363] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/16/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Remdesivir (REM) is an antiviral drug, which exercises its effect by targeting specifically RNA-dependent RNA polymerase. The interaction of REM with calf thymus DNA (CT-DNA) was investigated by multi-spectroscopic techniques (UV-Vis, fluorescence, circular dichroism and 31P NMR) in combination with different biophysical experiments and metadynamics simulation studies. UV-Vis and fluorescence spectroscopic analysis indicated formation of a complex between REM and CT-DNA, whose binding constant is in the order of 104 M-1. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 shown that REM binds to CT-DNA via intercalation mode. Significant alteration in the band due to base stacking pairs at 274 nm in the circular dichroism spectrum, appreciable increase in relative viscosity of the biomolecule upon binding with REM and the results of potassium iodide quenching studies confirmed that REM intercalates into the base pairs of CT-DNA. Thermodynamic parameters revealed that the binding of REM to CT-DNA is a spontaneous process (ΔG0 < 0) and the main force which holds them together in the REM/CT-DNA complex is electrostatic interaction (ΔH0 < 0 and ΔS0 > 0). The up-field shift in the 31P NMR signal of REM on interaction with CT-DNA suggested that phenyl ring adjacent to the phosphate moiety of REM may involve in the intercalation process. This is well supported by the analysis of free energy surface landscape derived from metadynamics simulation studies.
Collapse
Affiliation(s)
- R Durga Priyadharshini
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India.
| |
Collapse
|
14
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
|
15
|
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.
Collapse
|
16
|
Liu H, Wang HC, Wu SY, Jia XH, Tang WZ. Interaction of diplacone and eriodictyol with DNA by multi-spectroscopic and molecular modelling methods. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
17
|
Durga Priyadharshini R, Ponkarpagam S, Vennila KN, Elango KP. Spectroscopic and theoretical evidences for the surface binding of voglibose drug with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120888. [PMID: 35063822 DOI: 10.1016/j.saa.2022.120888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Binding of voglibose (VOG), an alpha glucosidase inhibitor, with CT-DNA has been investigated using various spectroscopic techniques including UV-Vis, fluorescence and circular dichroism (CD) coupled with relative viscosity. Isothermal titration calorimetric studies have been used to calculate the thermodynamic parameters such as ΔH (0.0188 cal/mol), ΔS (63.3 cal/mol/K) and ΔG (-18.8 kcal/mol), which reveal that the binding is a spontaneous process and hydrophobic and H-bonding interactions play major roles in the binding process. Effect of ionic strength confirms the existence of hydrophobic interaction between VOG and CT-DNA. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 suggest that VOG possibly binds on the surface of CT-DNA. Viscosity measurements also disclose that the binding could be mainly surface binding. Corroborating the experimental observations, metadynamics molecular simulation studies confirm that VOG binding on the surface of the DNA molecule through hydrophobic interactions and direct and water molecule mediated H-bonding.
Collapse
Affiliation(s)
- R Durga Priyadharshini
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India
| | - S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Gan C, Cheng R, Cai K, Wang X, Xie C, Xu T, Yuan C. Interaction of calf thymus DNA and glucose-based gemini cationic surfactants with different spacer length: A spectroscopy and DLS study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120606. [PMID: 34802935 DOI: 10.1016/j.saa.2021.120606] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
The interactions between calf thymus DNA and a series of glucose-based cationic gemini surfactants 1a-1c with different spacer length, n = 4, 6 and 8, were studied by UV absorption, fluorescence spectroscopy, circular dichroism, FT-IR, dynamic light scattering and zeta potential measurements. The results showed that all the surfactants could interact with DNA efficiently. On addition of increasing concentration of the surfactants, UV absorption hypochromicity with insignificant blue shift were observed, until the DNA signal disappeared. The surfactant 1c was more efficient in the reduction of absorption intensity of DNA. According to the fluorescence quenching experiments by ethidium bromide exclusion, 1c exhibited the highest binding properties, with the binding constant at 3.25 × 108 L·mol-1. The spectroscopy study indicated that the surfactants bound with the DNA by a non-intercalative mode, mainly electrostatic interaction between the positively charged headgroups of the surfactants and negatively charged phosphate groups of DNA at low concentration, and the hydrophobic interaction among the alkyl chains at high concentration. The conformation of DNA during the interaction process could be kept B-form of DNA. For 1c, the DNA molecules can be compacted to about 103 nm in hydrodynamic diameter at 0.2 mM, while the minimum sizes of DNA were 140 nm and 133 nm, respectively, in the presence of 1a and 1b. The impact of the cationic gemini surfactants on the DNA compaction and condensation would shed light on their potential applications in gene delivery.
Collapse
Affiliation(s)
- Changsheng Gan
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China.
| | - Rong Cheng
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China
| | - Kunliang Cai
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China
| | - Xiaonan Wang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China
| | - Chenkun Xie
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China
| | - Tiantian Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China
| | - Chuanxun Yuan
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, PR China
| |
Collapse
|
20
|
Ameen F, Siddiqui S, Jahan I, Nayeem SM, Rehman SU, Tabish M. Studying the interaction of scopolamine with calf-thymus DNA: An in-vitro and in-silico approach and genotoxicity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120391. [PMID: 34571375 DOI: 10.1016/j.saa.2021.120391] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Scopolamine is used to treat various CNS disorder like urinary incontinence, motion sickness, spasmic movements. Despite its pharmaceutical properties, its interaction with DNA is not yet reported. In this article, the interaction between scopolamine and ct-DNA is reported using a combination of biophysical techniques. UV-visible and steady-state fluorescence spectroscopy were used to study interaction and complex formation. Competitive displacement assays and potassium iodide quenching confirmed the mode of binding between scopolamine and DNA. Structural changes induced in the ct-DNA in the presence of scopolamine were evaluated by CD spectroscopy. The plasmid nicking and NBT assay confirmed the genotoxic effect of scopolamine. In-silico study by molecular docking and molecular dynamics simulation revealed the mode of interaction, major stabilizing forces as well as the nucleotide sequences to which the scopolamine binds.
Collapse
Affiliation(s)
- Faisal Ameen
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Sharmin Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Ishrat Jahan
- Department of Chemistry, Faculty of Science, A.M. University, Aligarh, U.P. 202002, India
| | - Shahid M Nayeem
- Department of Chemistry, Faculty of Science, A.M. University, Aligarh, U.P. 202002, India
| | - Sayeed Ur Rehman
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India.
| |
Collapse
|
21
|
|
22
|
Zangeneh Monfared F, Shahabadi N, Mahmoudi Hashemi M, Meibodi FS, Mirjafari Z. Studies of Ponceau 4R food colorant and zinc oxide nanoparticles containing it interactions with DNA and evaluation of their antimicrobial activity. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.16222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry Razi University Kermanshah Iran
- Center of Medical Biology Research (MBRC) Kermanshah University of Medical Sciences Kermanshah Iran
| | | | - Farhat Sadat Meibodi
- Department of Organic Chemistry, Faculty of Chemistry Razi University Kermanshah Iran
| | - Zohreh Mirjafari
- Department of Chemistry, Science and Research Branch Islamic Azad University Tehran Iran
| |
Collapse
|
23
|
Nematollahzadeh A, Mirzaei-Kalar Z, Abolhasani H, Babapoor A. Synthesize and multi-spectroscopic studies of zinc-naproxen nanodrug as DNA intercalator agent. Anal Biochem 2021; 642:114454. [PMID: 34774837 DOI: 10.1016/j.ab.2021.114454] [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: 05/26/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/27/2022]
Abstract
The zinc-naproxen complex as a nano-drug (NanoD) was synthesized successfully via fast and effective ultrasound-assisted processes. The chemicophysical properties of the NanoD were determined using FT-IR, XRD, SEM, and EDX mapping analyses. The results confirmed the formation of the 55 nm NanoD laminates. The interaction of the obtained NanoD with calf thymus deoxyribonucleic acid (CT-DNA) was studied as well. Structural and topography changes of DNA in interaction with the NanoD were investigated by atomic force microscopy (AFM). The results of electronic absorption spectroscopy, the DNA-viscosity studies, and competition fluorescence spectroscopy showed that CT-DNA binds to the NanoD through the intercalative binding mode. The data of AFM analysis indicated swollen CT-DNA upon interaction with the NanoD. The in vitro investigation of cytotoxicity of the NanoD on HT-29 and Hep G2 cancer cells demonstrated high cytotoxicity activity of the NanoD than that of cisplatin in HT-29 cell line, especially at lower concentrations.
Collapse
Affiliation(s)
- Ali Nematollahzadeh
- Department of Chemical Engineering, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil, Iran.
| | - Zeinab Mirzaei-Kalar
- Department of Advanced Technologies, University of Mohaghegh Ardabili, Namin, Ardabil, Iran
| | - Hoda Abolhasani
- Cellular and Molecular Research Center and Faculty of Medicine, Qom University of Medical Sciences, Qom, Iran
| | - Aziz Babapoor
- Department of Chemical Engineering, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil, Iran
| |
Collapse
|
24
|
Deciphering the DNA-binding affinity, cytotoxicity and apoptosis induce as the anticancer mechanism of Bavachinin: An experimental and computational investigation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
25
|
Coban B, Saka E, Yıldız U, Akkoç S. DNA Interactions and Antiproliferative Activity Studies of Octahedral Nickel Complexes of Two Extended Phenanthrolines. ChemistrySelect 2021. [DOI: 10.1002/slct.202102376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Burak Coban
- Department of Chemistry Faculty of Arts and Sciences Zonguldak Bülent Ecevit University Zonguldak 67100 Turkey
| | - Engin Saka
- Department of Chemistry Faculty of Arts and Sciences Zonguldak Bülent Ecevit University Zonguldak 67100 Turkey
| | - Ufuk Yıldız
- Department of Chemistry Faculty of Arts and Sciences Zonguldak Bülent Ecevit University Zonguldak 67100 Turkey
| | - Senem Akkoç
- Department of Basic Pharmaceutical Sciences Faculty of Pharmacy Süleyman Demirel University Isparta 32260 Turkey
| |
Collapse
|
26
|
Shahabadi N, Shiri F, Hadidi S, Farshadfar K, Darbemamieh M, Mark Roe S. The role of both intercalation and groove binding at AT-rich DNA regions in the interaction process of a dinuclear Cu(I) complex probed by spectroscopic and simulation analysis. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116290] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
27
|
Zangeneh monfared F, Shahabadi N, Mahmoudi Hashemi M, Sadat Meibodi F, Mirjafari Z. Zinc oxide nanoparticles coated with food colorant Brilliant black: Synthesis, characterization, and comparative DNA interaction and antibacterial activity studies. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry Razi University Kermanshah Iran
- Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences Kermanshah Iran
| | | | - Farhat Sadat Meibodi
- Department of Organic Chemistry, Faculty of Chemistry Razi University Kermanshah Iran
| | - Zohreh Mirjafari
- Department of Chemistry, Science and Research Branch Islamic Azad University Tehran Iran
| |
Collapse
|
28
|
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: 9] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
29
|
Mbaba M, Dingle LMK, Zulu AI, Laming D, Swart T, de la Mare JA, Hoppe HC, Edkins AL, Khanye SD. Coumarin-Annulated Ferrocenyl 1,3-Oxazine Derivatives Possessing In Vitro Antimalarial and Antitrypanosomal Potency. Molecules 2021; 26:1333. [PMID: 33801371 PMCID: PMC7958634 DOI: 10.3390/molecules26051333] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022] Open
Abstract
A tailored series of coumarin-based ferrocenyl 1,3-oxazine hybrid compounds was synthesized and investigated for potential antiparasitic activity, drawing inspiration from the established biological efficacy of the constituent chemical motifs. The structural identity of the synthesized compounds was confirmed by common spectroscopic techniques: NMR, HRMS and IR. Biological evaluation studies reveal that the compounds exhibit higher in vitro antiparasitic potency against the chemosensitive malarial strain (3D7 P. falciparum) over the investigated trypanosomiasis causal agent (T. b. brucei 427) with mostly single digit micromolar IC50 values. When read in tandem with the biological performance of previously reported structurally similar non-coumarin, phenyl derivatives (i.e., ferrocenyl 1,3-benzoxazines and α-aminocresols), structure-activity relationship analyses suggest that the presence of the coumarin nucleus is tolerated for biological activity though this may lead to reduced efficacy. Preliminary mechanistic studies with the most promising compound (11b) support hemozoin inhibition and DNA interaction as likely mechanistic modalities by which this class of compounds may act to produce plasmocidal and antitrypanosomal effects.
Collapse
Affiliation(s)
- Mziyanda Mbaba
- Department of Chemistry, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (M.M.); (A.I.Z.)
| | - Laura M. K. Dingle
- Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (L.M.K.D.); (D.L.); (T.S.); (J.-A.d.l.M.); (H.C.H.); (A.L.E.)
- Biomedical Biotechnology Research Unit, Rhodes University, Makhanda 6140, South Africa
| | - Ayanda I. Zulu
- Department of Chemistry, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (M.M.); (A.I.Z.)
| | - Dustin Laming
- Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (L.M.K.D.); (D.L.); (T.S.); (J.-A.d.l.M.); (H.C.H.); (A.L.E.)
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Makhanda 6140, South Africa
| | - Tarryn Swart
- Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (L.M.K.D.); (D.L.); (T.S.); (J.-A.d.l.M.); (H.C.H.); (A.L.E.)
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Makhanda 6140, South Africa
| | - Jo-Anne de la Mare
- Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (L.M.K.D.); (D.L.); (T.S.); (J.-A.d.l.M.); (H.C.H.); (A.L.E.)
- Biomedical Biotechnology Research Unit, Rhodes University, Makhanda 6140, South Africa
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Makhanda 6140, South Africa
| | - Heinrich C. Hoppe
- Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (L.M.K.D.); (D.L.); (T.S.); (J.-A.d.l.M.); (H.C.H.); (A.L.E.)
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Makhanda 6140, South Africa
| | - Adrienne L. Edkins
- Department of Biochemistry and Microbiology, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (L.M.K.D.); (D.L.); (T.S.); (J.-A.d.l.M.); (H.C.H.); (A.L.E.)
- Biomedical Biotechnology Research Unit, Rhodes University, Makhanda 6140, South Africa
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Makhanda 6140, South Africa
| | - Setshaba D. Khanye
- Department of Chemistry, Faculty of Science, Rhodes University, Makhanda 6140, South Africa; (M.M.); (A.I.Z.)
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Makhanda 6140, South Africa
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Rhodes University, Makhanda 6140, South Africa
| |
Collapse
|
30
|
Hansda S, Mitra A, Ghosh R. Studies to explore the UVA photosensitizing action of 9-phenylacridine in cells by interaction with DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:393-422. [PMID: 33586599 DOI: 10.1080/15257770.2021.1880011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Acridine and its derivatives are well known for their DNA binding properties. In this report, we present our findings on evaluating different binding parameters of the interaction of 9-phenylacridine (ACPH) with DNA. Absorption spectroscopic studies including standard and reverse titration, the effects of ionic strength and temperature on titration, and Job plot analysis were done to calculate the binding constant and determine the different thermodynamic parameters and stoichiometry of the binding. Spectrofluorimetry and circular dichroism (CD) spectral titration were also utilized to confirm these findings. The results indicated that ACPH binds to DNA reversibly through non-electrostatic interactions by hydrogen bonding and van der Waals interactions. The binding constant and the number of binding sites were of the order 103 M-1 and ≈2, respectively with a binding stoichiometry of 1:4. The binding of ACPH with DNA was spontaneous, exothermic and enthalpy-driven. The extent of uptake of ACPH in B16 melanoma cells was estimated. As this compound absorbs in the UVA region, the effect of treatment with ACPH prior to UVA exposure was assessed to evaluate its phototoxicity in these cells. Our results indicated that the binding to DNA enhanced damage to sensitize cells to killing through apoptosis. Our findings indicated its potential to act as a photosensitizer.
Collapse
Affiliation(s)
- Surajit Hansda
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | - Anindita Mitra
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | - Rita Ghosh
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| |
Collapse
|
31
|
Experimental and computational studies of the interaction of gemifloxacin and manganese (II) gemifloxacin complex with DNA. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
32
|
Priya Velammal S, Peter Amaladhas T. Biofunctionalized silver and gold nanoparticles as potential curative agents. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Subramanian Priya Velammal
- Post Graduate and Research Department of Chemistry V.O. Chidambaram College Tuticorin Tamil Nadu 628008 India
| | - Thomas Peter Amaladhas
- Post Graduate and Research Department of Chemistry V.O. Chidambaram College Tuticorin Tamil Nadu 628008 India
| |
Collapse
|
33
|
Evaluation of Antioxidant, Anticancer and DNA Binding Potentials of Noble Metal Nanoparticles Synthesized Using Aristolochia indica and Indigofera tinctoria. J CLUST SCI 2020. [DOI: 10.1007/s10876-020-01858-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
34
|
Yadav N, Singh A, Kaushik M. Hydrothermal synthesis and characterization of magnetic Fe 3O 4 and APTS coated Fe 3O 4 nanoparticles: physicochemical investigations of interaction with DNA. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2020; 31:68. [PMID: 32705385 DOI: 10.1007/s10856-020-06405-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
Magnetic nanoparticles (MNPs) especially iron oxide (Fe3O4) NPs have quite extensively been used for in vivo delivery of biomolecules and drugs because of their high bioconjugation efficiency. In this study, Fe3O4 NPs and (3-Aminopropyl) triethoxysilane (APTS) coated Fe3O4 NPs were synthesized and their interaction with Calf thymus (Ct) DNA has been studied in order to understand their usage in biomedical applications. Hydrothermal method was used for the NPs synthesis. Characterization of NPs was done using techniques like UV-Visible spectroscopy, FTIR spectroscopy, FE-SEM, EDAX, Zeta Sizer and powder XRD. Further, interaction studies of NPs with Ct-DNA were investigated using various physicochemical techniques. In UV-Visible studies, hypochromicity with binding constant 3.2 × 105 M-1 was observed. Binding constants calculated using fluorescence studies were found to be k = 3.2 × 104 M-1, 2.9 × 104 M-1 at 293 and 323 K respectively. Results of UV-Visible and fluorescence studies were in correlation with other techniques like UV-TM and CD. All studies suggested alteration in DNA conformation on interaction with surface engineered Fe3O4 NPs, stabilizing DNA-NPs conjugate via partial intercalation and electrostatic interactions. This study may facilitate our understanding regarding the physicochemical properties and DNA-binding ability of APTS-Fe3O4 NPs for their further application in magnetosensitive biosensing and drug delivery. Iron oxide based magnetic nanoparticles are well known for their excellent bio-conjugation efficiency and therefore APTS-Fe3O4 NPs were synthesized via very simple and benign hydrothermal method. Further, the interaction of APTS-Fe3O4 NPs with calf thymus DNA was studied using various physicochemical techniques to explore their potential in biomedical applications.
Collapse
Affiliation(s)
- Neelam Yadav
- Nano-bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India
- Department of Chemistry, University of Delhi, Delhi, India
| | - Amit Singh
- Nano-bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India
- Department of Chemistry, University of Delhi, Delhi, India
| | - Mahima Kaushik
- Nano-bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India.
| |
Collapse
|
35
|
Shahabadi N, Shiri F, Hadidi S, Farshadfar K, Sajadimajd S, Roe SM. Equilibrium and site selective analysis for DNA threading intercalation of a new phosphine copper(I) complex: Insights from X-ray analysis, spectroscopic and molecular modeling studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 235:118280. [PMID: 32248034 DOI: 10.1016/j.saa.2020.118280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/18/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
To clarify the interaction of phosphine copper(I) complex with DNA, our study reports the synthesis of a new phosphine copper(I) complex, along with a detailed analysis of the geometry characterization and its interaction with double-stranded DNA. The triclinic phase Cu(PPh3)2(L)(I) with a tetrahedral geometry was identified as the product of the reaction of copper(I) iodide with (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] ligand and triphenylphosphine by single-crystal X-ray analysis. Molecular interaction of the synthesized complex with the calf thymus deoxyribonucleic acid (ct-DNA) was investigated in the physiological buffer (pH 7.4) by multi-spectroscopic approaches associated with a competitive displacement towards Hoechst 33258 and methylene blue (MB) as groove and intercalator probes. The fluorescence and UV/Vis results detected the formation of a complex-DNA adduct in the ground-state with a binding affinity in order of 104 M-1, which is in keeping with both groove binders and intercalators. The thermodynamic parameters, ΔS0 = -200.31 ± 0.08 cal/mol·K and ΔH0 = -63.11 ± 0.24 kcal/mol, confirmed that the van der Waals interaction is the main driving force for the binding process. Moreover, the ionic strength and pH effect experiments demonstrated the electrostatic interactions between the complex and DNA is negligible. Analysis of the molecular docking simulation declared the flat (E,E)-N,N'-1,2-Ethanediylbis[1-(3-pyridinyl)methanimine] part of the complex was inserted between the sequential A…T/A…T base pairs, while the phosphine substituents were located in the groove, i.e. threading intercalation. Besides, the cytotoxicity of the complex against the MCF-7 human breast cancer cells was detected at IC50 = 10 μg/mL.
Collapse
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Kaveh Farshadfar
- Department of Chemistry, Islamic Azad University, Central Tehran Branch, Poonak, Tehran 1469669191, Iran
| | | | - S Mark Roe
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| |
Collapse
|
36
|
Wani TA, Alsaif N, Bakheit AH, Zargar S, Al-Mehizia AA, Khan AA. Interaction of an abiraterone with calf thymus DNA: Investigation with spectroscopic technique and modelling studies. Bioorg Chem 2020; 100:103957. [DOI: 10.1016/j.bioorg.2020.103957] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/11/2023]
|
37
|
Mbaba M, Dingle LMK, Swart T, Cash D, Laming D, de la Mare JA, Taylor D, Hoppe HC, Biot C, Edkins AL, Khanye SD. The in Vitro Antiplasmodial and Antiproliferative Activity of New Ferrocene-Based α-Aminocresols Targeting Hemozoin Inhibition and DNA Interaction. Chembiochem 2020; 21:2643-2658. [PMID: 32307798 DOI: 10.1002/cbic.202000132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/15/2020] [Indexed: 01/30/2023]
Abstract
The conjugation of organometallic complexes to known bioactive organic frameworks is a proven strategy revered for devising new drug molecules with novel modes of action. This approach holds great promise for the generation of potent drug leads in the quest for therapeutic chemotypes with the potential to overcome the development of clinical resistance. Herein, we present the in vitro antiplasmodial and antiproliferative investigation of ferrocenyl α-aminocresol conjugates assembled by amalgamation of the organometallic ferrocene unit and an α-aminocresol scaffold possessing antimalarial activity. The compounds pursued in the study exhibited higher toxicity towards the chemosensitive (3D7) and -resistant (Dd2) strains of the Plasmodium falciparum parasite than to the human HCC70 triple-negative breast cancer cell line. Indication of cross-resistance was absent for the compounds evaluated against the multi-resistant Dd2 strain. Structure-activity analysis revealed that the phenolic hydroxy group and rotatable σ bond between the α-carbon and NH group of the α-amino-o-cresol skeleton are crucial for the biological activity of the compounds. Spectrophotometric techniques and in silico docking simulations performed on selected derivatives suggest that the compounds show a dual mode of action involving hemozoin inhibition and DNA interaction via minor-groove binding. Lastly, compound 9 a, identified as a possible lead, exhibited preferential binding for the plasmodial DNA isolated from 3D7 P. falciparum trophozoites over the mammalian calf thymus DNA, thereby substantiating the enhanced antiplasmodial activity of the compounds. The presented research demonstrates the strategy of incorporating organometallic complexes into known biologically active organic scaffolds as a viable avenue to fashion novel multimodal compounds with potential to counter the development drug resistance.
Collapse
Affiliation(s)
- Mziyanda Mbaba
- Faculty of Science, Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa
| | - Laura M K Dingle
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.,Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa
| | - Tarryn Swart
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.,Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Devon Cash
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.,Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa
| | - Dustin Laming
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.,Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Jo-Anne de la Mare
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.,Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa.,Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Dale Taylor
- Faculty of Medicine, Division of Clinical Pharmacology, University of Cape Town Observatory, Cape Town, 7925, South Africa
| | - Heinrich C Hoppe
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.,Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Christophe Biot
- Université de Lille, CNRS, UMR 8576 UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Adrienne L Edkins
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.,Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa.,Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Setshaba D Khanye
- Faculty of Science, Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa.,Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa.,Faculty of Pharmacy, Division of Pharmaceutical Chemistry, Rhodes University, Grahamstown, 6140, South Africa
| |
Collapse
|
38
|
Dareini M, Amiri Tehranizadeh Z, Marjani N, Taheri R, Aslani-Firoozabadi S, Talebi A, NayebZadeh Eidgahi N, Saberi MR, Chamani J. A novel view of the separate and simultaneous binding effects of docetaxel and anastrozole with calf thymus DNA: Experimental and in silico approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117528. [PMID: 31718965 DOI: 10.1016/j.saa.2019.117528] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
DNA stands as the primary purpose of many anticancer drugs and according to the performed research on this field, some certain changes contain crucial functionalities in the regulated transcription of DNA. Therefore, the interaction between anticancer drugs and DNA play an important role in understanding their function and also provide a better groundwork for producing more efficient and newer drugs. Here, the interaction between Docetaxel (DO) and calf thymus DNA (ct DNA), in the presence and absence of Anastrozole (AN), has been examined through the usage of different methods that include isothermal titration calorimetry, multi-spectroscopic, viscometry, and molecular docking techniques. Interaction studies have been performed by preparing different molar ratios of DO with the constant ct DNA and AN concentration at pH = 6.8. The binding constants have been calculated to be 7.93 × 104 M-1 and 6.27 × 104 M-1, which indicate the strong binding of DO with ct DNA double helix in the absence and presence of AN, respectively. Thermodynamic parameters, which were obtained from fluorescence spectroscopy and isothermal titration calorimetry, have suggested that the binding of DO and AN to ct DNA as binary and ternary systems have been mainly driven by the electrostatic interactions. The relative viscosity of ct DNA has increased upon the addition of DO and AN, which confirms the interaction mode. A competitive binding study has reported that the enhanced emission intensity of ethidium bromide (EB) and acridine orange (AO), in the presence of ct DNA, have been quenched through the addition of DO and Anastrozole as binary and ternary systems. As it is indicated by these findings, DO is capable of displacing EB and AO from their binding site in ct DNA; hence, it can be concluded that DO and AN are able to intercalate into the base pairs of ct DNA in binary and ternary systems. Molecular docking studies have corroborated the mentioned experimental results.
Collapse
Affiliation(s)
- Maryam Dareini
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Narges Marjani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Reza Taheri
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Atiye Talebi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Negar NayebZadeh Eidgahi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mohammad Reza Saberi
- Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
| |
Collapse
|
39
|
Paul P, Mati SS, Kumar GS. Insights on the interaction of phenothiazinium dyes methylene blue and new methylene blue with synthetic duplex RNAs through spectroscopy and modeling. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 204:111804. [PMID: 32007677 DOI: 10.1016/j.jphotobiol.2020.111804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/31/2022]
Abstract
The ubiquitous influence of double stranded RNAs in biological events makes them imperative to gather data based on specific binding procedure of small molecules to various RNA conformations. Particular interest may be attributed to situations wherein small molecules target RNAs altering their structures and causing functional modifications. The main focus of this study is to delve into the interactive pattern of two small molecule phenothiazinium dyes, methylene blue and new methylene blue, with three duplex RNA polynucleotides-poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C) by spectroscopic and molecular modeling techniques. Analysis of data as per Scatchard and Benesi-Hildebrand methodologies revealed highest affinity of these dyes to poly(A).poly(U) and least to poly(I).poly(C). In addition to fluorescence quenching, viscometric studies also substantiated that the dyes follow different modes of binding to different RNA polynucleotides. Distortion in the RNA structures with induced optical activity in the otherwise optically inactive dye molecules was evidenced from circular dichroism results. Dye-induced RNA structural modification occurred from extended conformation to compact particles visualized by atomic force microscopy. Molecular docking results revealed different binding patterns of the dye molecules within the RNA duplexes. The novelty of the present work lies towards a new contribution of the phenothiazinium dyes in dysfunctioning double stranded RNAs, advancing our knowledge to their potential use as RNA targeted small molecules.
Collapse
Affiliation(s)
- Puja Paul
- Department of Chemistry, Dinabandhu Mahavidyalaya, Bongaon, West Bengal 743235, India; CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Soumya Sundar Mati
- Government GD College, Keshiary, Paschim Medinipur, West Bengal 721135, India
| | | |
Collapse
|
40
|
Mbaba M, Dingle LMK, Cash D, Mare JADL, Laming D, Taylor D, Hoppe HC, Edkins AL, Khanye SD. Repurposing a polymer precursor: Synthesis and in vitro medicinal potential of ferrocenyl 1,3-benzoxazine derivatives. Eur J Med Chem 2019; 187:111924. [PMID: 31855792 DOI: 10.1016/j.ejmech.2019.111924] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 01/12/2023]
Abstract
Cancer and malaria remain relevant pathologies in modern medicinal chemistry endeavours. This is compounded by the threat of development of resistance to existing clinical drugs in use as first-line option for treatment of these diseases. To counter this threat, strategies such as drug repurposing and hybridization are constantly adapted in contemporary drug discovery for the expansion of the drug arsenal and generation of novel chemotypes with potential to avert or delay resistance. In the present study, a polymer precursor scaffold, 1,3-benzoxazine, has been repurposed by incorporation of an organometallic ferrocene unit to produce a novel class of compounds showing in vitro biological activity against breast cancer, malaria and trypanosomiasis. The resultant ferrocenyl 1,3-benzoxazine compounds displayed high potency and selectivity against the investigated diseases, with IC50 values in the low and sub-micromolar range against both chloroquine-sensitive (3D7) and resistant (Dd2) strains of the Plasmodium falciparum parasite. On the other hand, antitrypanosomal (Trypanosoma brucei brucei) potencies were observed between 0.15 and 38.6 μM. The majority of the compounds were not active against breast cancer cells (HCC70), however, for the toxic compounds, IC50 values ranged from 11.0 to 30.5 μM. Preliminary structure-activity relationships revealed the basic oxazine sub-ring and lipophilic benzene substituents to be conducive for biological efficacy of the ferrocenyl 1,3-benzoxazines reported in the study. DNA interaction studies performed on the most promising compound 4c suggested that DNA damage may be one possible mode of action of this class of compounds.
Collapse
Affiliation(s)
- Mziyanda Mbaba
- Faculty of Science, Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa.
| | - Laura M K Dingle
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa; Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa
| | - Devon Cash
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa; Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa
| | - Jo-Anne de la Mare
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa; Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Dustin Laming
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Dale Taylor
- Division of Clinical Pharmacology, Faculty of Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Heinrich C Hoppe
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Adrienne L Edkins
- Faculty of Science, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa; Biomedical Biotechnology Research Unit, Rhodes University, Grahamstown, 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa
| | - Setshaba D Khanye
- Faculty of Science, Department of Chemistry, Rhodes University, Grahamstown, 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown, 6140, South Africa; Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Rhodes University, Grahamstown, 6140, South Africa.
| |
Collapse
|
41
|
Exploring the DNA binding efficacy of Cobalt(II) and Copper(II) complexes of hydroxamic acids and explicating their anti-cancer propensity. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
42
|
Kou SB, Lou YY, Zhou KL, Wang BL, Lin ZY, Shi JH. In vitro exploration of interaction behavior between calf thymus DNA and fenhexamid with the help of multi-spectroscopic methods and molecular dynamics simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.112067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
43
|
Zhang Q, Peng Q, Shu X, Mo D, Jiang D. Spectroscopic analysis of tylosin adsorption on extracellular DNA reveals its interaction mechanism. Colloids Surf B Biointerfaces 2019; 183:110431. [PMID: 31421405 DOI: 10.1016/j.colsurfb.2019.110431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
Extracellular DNA (eDNA), which is commonly detected in aquatic and terrestrial environments, may be involved in gene transfer, increases in genetic diversity, and evolution. However, it has been reported that some small organic molecules or heavy metal ions can influence the transformation of DNA and even destroy its structure. We previously found that tylosin (TYL, a kind of antibiotic) is adsorbed onto salmon sperm DNA in a mixed solution. However, it is not clear whether this antibiotic affects the structure of DNA, and the mechanism of their interaction needs to be clarified. Therefore, we investigated the adsorption of TYL on different concentrations of salmon sperm DNA using agarose gel electrophoresis, ultraviolet-visible (UV-vis) spectroscopy, fluorescence spectroscopy, and surface enhanced Raman spectroscopy (SERS) to elucidate the interaction mechanism between TYL and DNA. The results showed that the adsorption of TYL decreased with increased concentrations of DNA. The electrophoresis band of pristine DNA was at 5000 bps. The brightness of the DNA band decreased with the TYL concentration and their incubation time. As the concentration of TYL increased, the fluorescence absorption intensity of DNA decreased significantly. Redshift and hyperchromicity were observed in the UV-vis adsorption spectrum with the presence of TYL in DNA solution, and they weakened as the DNA concentration increased. The Raman spectrum intensities of characteristic peaks in the mixed solution were weaker than that of pure TYL solution, and the peak intensity increased with increasing DNA concentration. Even a part of TYL characteristic peaks disappeared in the mixed solution. These results indicated that the pyran and macrolide of TYL might intercalate into the base pair plane of DNA. In addition, electrostatic attraction between TYL and DNA and interactions among TYL molecules may also play a role in the interaction mechanism. However, the double helix structure of DNA was not subject to the interaction of TYL.
Collapse
Affiliation(s)
- Qian Zhang
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
| | - Qiuyan Peng
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin, Guangxi, 541000, China
| | - Xiaohua Shu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, Guangxi, 541000, China.
| | - Deqing Mo
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
| | - Dongyun Jiang
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
| |
Collapse
|
44
|
Synthesis and characterization of hydrothermally synthesized superparamagnetic APTS–ZnFe2O4 nanoparticles: DNA binding studies for exploring biomedical applications. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00953-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
45
|
Shahabadi N, Shiri F, Hadidi S. Studies on the interaction of antibiotic drug rifampin with DNA and influence of bivalent metal ions on binding affinity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 219:195-201. [PMID: 31035130 DOI: 10.1016/j.saa.2019.04.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/21/2019] [Accepted: 04/21/2019] [Indexed: 06/09/2023]
Abstract
In this paper, the interaction between rifampin, a known antibiotic used against tuberculosis, and DNA helix is investigated by applying multiple biophysical and molecular modelling approaches in an aqueous solution at pH 7.4 and 5. It was proved that the fluorescence quenching of labeled probe DNA by rifampin is a result of the complex formation of rifampin in groove of DNA. Binding parameters were calculated using the logarithmic Hill equation to provide a quantitative term of the binding affinity between rifampin and DNA sites. The resulting ΔH0 = -122.76 ± 0.07 kJ/mol and ΔS0 = -308.19 ± 238.78 J/mol K confirms the role of the Van der Waals' forces and hydrogen bonding in the rifampin-DNA complexation. Furthermore, the influence of bivalent metal ions on the binding affinity was resulted in order of Cu(II) > Ca(II) > Co(II) > Zn(II).
Collapse
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran; Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
46
|
Wumaier M, Shi JJ, Yao TM, Hu XC, Gao RR, Shi S. G-quadruplex and duplex DNA binding studies of novel Ruthenium(II) complexes containing ascididemin ligands. J Inorg Biochem 2019; 196:110681. [DOI: 10.1016/j.jinorgbio.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: 11/24/2018] [Revised: 03/22/2019] [Accepted: 03/27/2019] [Indexed: 11/29/2022]
|
47
|
Agrawal R, Siddiqi MK, Thakur Y, Tripathi M, Asatkar AK, Khan RH, Pande R. Explication of bovine serum albumin binding with naphthyl hydroxamic acids using a multispectroscopic and molecular docking approach along with its antioxidant activity. LUMINESCENCE 2019; 34:628-643. [PMID: 31190435 DOI: 10.1002/bio.3645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/16/2022]
Abstract
In the present investigation, the protein-binding properties of naphthyl-based hydroxamic acids (HAs), N-1-naphthyllaurohydroxamic acid (1) and N-1-naphthyl-p-methylbenzohydroxamic acid (2) were studied using bovine serum albumin (BSA) and UV-visible spectroscopy, fluorescence spectroscopy, diffuse reflectance spectroscopy-Fourier transform infrared (DRS-FTIR), circular dichroism (CD), and cyclic voltammetry along with computational approaches, i.e. molecular docking. Alteration in the antioxidant activities of compound 1 and compound 2 during interaction with BSA was also studied. From the fluorescence studies, thermodynamic parameters such as Gibb's free energy (ΔG), entropy change (ΔS) and enthalpy change (ΔH) were calculated at five different temperatures (viz., 298, 303, 308, 313 or 318 K) for the HAs-BSA interaction. The results suggested that the binding process was enthalpy driven with dominating hydrogen bonds and van der Waals' interactions for both compounds. Warfarin (WF) and ibuprofen (IB) were used for competitive site-specific marker binding interaction and revealed that compound 1 and compound 2 were located in subdomain IIA (Sudlow's site I) on the BSA molecule. Conclusions based on above-applied techniques signify that various non-covalent forces were involved during the HAs-BSA interaction. Therefore the resulted HAs-BSA interaction manifested its effect in transportation, distribution and metabolism for the drug in the blood circulation system, therefore establishing HAs as a drug-like molecule.
Collapse
Affiliation(s)
- Rainy Agrawal
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | | | - Yamini Thakur
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - Mamta Tripathi
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | | | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India
| | - Rama Pande
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| |
Collapse
|
48
|
Similarities and differences in d 6 low-spin ruthenium, rhodium and iridium half-sandwich complexes: synthesis, structure, cytotoxicity and interaction with biological targets. J Biol Inorg Chem 2019; 24:591-606. [PMID: 31115765 PMCID: PMC6598960 DOI: 10.1007/s00775-019-01665-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/08/2019] [Indexed: 11/27/2022]
Abstract
In this paper, we discussed the similarities and differences in d6 low-spin half-sandwich ruthenium, rhodium and iridium complexes containing 2,2′-biimidazole (H2biim). Three new complexes, {[RuCl(H2biim)(η6-p-cymene)]PF6}2·H2O (1), [(η5-Cp)RhCl(H2biim)]PF6 (2), and [(η5-Cp)IrCl(H2biim)]PF6 (3), were fully characterized by CHN, X-ray diffraction analysis, UV–Vis, FTIR, and 1H, 13C and 15N NMR spectroscopies. The complexes exhibit a typical pseudooctahedral piano-stool geometry, in which the aromatic arene ring (p-cymene or Cp) forms the seat, while the bidentate 2,2′-biimidazole and chloride ion form the three legs of the piano stool. Moreover, the cytotoxic activities of the compounds were examined in the LoVo, HL-60, MV-4-11, MCF-7 human cancer cell lines and BALB/3T3 normal mouse fibroblasts. Notably, the investigated complexes showed no cytotoxic effects towards the normal BALB/3T3 cell line compared to cisplatin, which has an IC50 value of 2.20 µg. Importantly, 1 displayed the highest activity against HL-60 (IC50 4.35 µg). To predict a binding mode, we explored the potential interactions of the metal complexes with CT-DNA and protein using UV absorption and circular dichroism. The obtained data suggest that the complexes could interact with CT-DNA via an outside binding mode. Moreover, binding of the complexes with the GSH via UV–Vis and ESI mass spectra was determined. Comparative studies have shown that the rhodium complex (2) is the most GSH reactive, which is probably responsible for its deactivation towards LoVo and MCF-7 tumour cells. The influence of the metal ion on the biological activity of isostructural Rh(III) and Ir(III) complexes was an important goal of the presented investigation.
Collapse
|
49
|
Shiri F, Hadidi S, Rahimi-Nasrabadi M, Ahmadi F, Ganjali MR, Ehrlich H. Synthesis, characterization and DNA binding studies of a new ibuprofen-platinum(II) complex. J Biomol Struct Dyn 2019; 38:1119-1129. [PMID: 31012380 DOI: 10.1080/07391102.2019.1597769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The study is focused on the synthesis of a novel complex of ibuprofen and Platinum(II). The formation of the product was characterized through analytical tools including Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance, ultraviolet-visible spectroscopy, mass spectrometry as well as density functional theory. Using the continuous variation method, the stoichiometry of Pt(HIb)2(Cl)2 binding on DNA (ct-DNA) determines as a single class of binding. Based on the results of Stern-Volmer analysis on the fluorescence quenching data, the quenching mechanism was determined to be static in nature. The studies indicated that the complex could bind DNA molecules via groove binding for four major reasons. Initially, the complex-DNA binding constant determined based on spectrophotometric data were found to be comparable to those of groove-binding drugs. In addition, the competitive fluorimetric based on the applications of Hoechst 33258 proved the ability of Pt(HIb)2(Cl)2 to displace with Hoechst in its DNA-bounded form, reflecting the competition between Pt(HIb)2(Cl)2 and Hoechst for groove binding. Further, no considerable changes were observed in the intensity of the methylene blue (MB)-DNA system after adding the Pt(HIb)2(Cl)2 complex, reflecting the stability of MB molecules in the DNA helix and a non-intercalative bonds of Pt(HIb)2(Cl)2 interaction on DNA. Finally, minor changes in the viscosity of DNA in the presence of Pt(HIb)2(Cl)2, indicated that changes in the length of DNA in the presence of the complex are negligible, supporting the assumption of DNA groove-binding. Also induced CD spectral changes and docking simulations were in favor of the groove mechanism for the Pt(HIb)2(Cl)2-DNA binding.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Farshad Shiri
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saba Hadidi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehdi Rahimi-Nasrabadi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Farhad Ahmadi
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, University of Tehran, Tehran, Iran.,Biosensor Research Centre, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | |
Collapse
|
50
|
Popov AB, Stolić I, Krstulović L, Taylor MC, Kelly JM, Tomić S, Tumir L, Bajić M, Raić-Malić S. Novel symmetric bis-benzimidazoles: Synthesis, DNA/RNA binding and antitrypanosomal activity. Eur J Med Chem 2019; 173:63-75. [PMID: 30986572 DOI: 10.1016/j.ejmech.2019.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/22/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
The novel benzimidazol-2-yl-fur-5-yl-(1,2,3)-triazolyl dimeric series with aliphatic and aromatic central linkers was successfully prepared with the aim of assessing binding affinity to DNA/RNA and antitrypanosomal activity. UV-Visible spectroscopy, thermal denaturation showed interaction of heterocyclic bis-amidines with ctDNA. Circular dichroism studies indicated uniform orientation of heterocyclic bis-amidines along the chiral double helix axis, revealing minor groove binding as the dominant binding mode. The amidino fragment and 1,4-bis(oxymethylene)phenyl spacer were the main determinants of activity against Trypanosoma brucei. The bis-benzimidazole imidazoline 15c, which had antitrypanosomal potency in the submicromolar range and DNA interacting properties, emerged as a candidate for further structural optimization to obtain more effective agents to combat trypanosome infections.
Collapse
Affiliation(s)
- A Bistrović Popov
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000, Zagreb, Croatia
| | - I Stolić
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000, Zagreb, Croatia
| | - L Krstulović
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000, Zagreb, Croatia
| | - M C Taylor
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - J M Kelly
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - S Tomić
- Division of Organic Chemistry and Biochemistry, Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10000, Zagreb, Croatia
| | - L Tumir
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Bijenička 54, HR-10000, Zagreb, Croatia
| | - M Bajić
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, HR-10000, Zagreb, Croatia
| | - S Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, HR-10000, Zagreb, Croatia.
| |
Collapse
|