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Biswas S, Basak S, Samui S, Pasadi S, Muniyappa K, Naskar J. Co‐Assembly of Peptide with G‐Quadruplex DNA: A Strategic Approach to Develop Anticancer Therapeutics. ChemistrySelect 2023. [DOI: 10.1002/slct.202203563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Soumi Biswas
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Shubhanwita Basak
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Satyabrata Samui
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Sanjeev Pasadi
- Department of Biochemistry Indian Institute of Science Bangalore Karnataka 560 012 India
| | - K. Muniyappa
- Department of Biochemistry Indian Institute of Science Bangalore Karnataka 560 012 India
| | - Jishu Naskar
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
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Sharifi-Rad A, Amiri-Tehranizadeh Z, Talebi A, Nosrati N, Medalian M, Pejhan M, Hamzkanloo N, Saberi MR, Mokaberi P, Chamani J. Multi spectroscopic and molecular simulation studies of propyl acridone binding to calf thymus DNA in the presence of electromagnetic force. BIOIMPACTS : BI 2023; 13:5-16. [PMID: 36817002 PMCID: PMC9923809 DOI: 10.34172/bi.2022.23592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 01/09/2023]
Abstract
Introduction: Here, the interaction behavior between propyl acridones (PA) and calf thymus DNA (ct-DNA) has been investigated to attain the features of the binding behavior of PA with ct-DNA, which includes specific binding sites, modes, and constants. Furthermore, the effects of PA on the conformation of ct-DNA seem to be quite significant for comprehending the medicine's mechanism of action and pharmacokinetics. Methods: The project was accomplished through means of absorbance studies, fluorescence spectroscopy, circular dichroism, viscosity measurement, thermal melting, and molecular modeling techniques. Results: The intercalation of PA has been suggested by fluorescence quenching and viscosity measurements results while the thermal melting and circular dichroism studies have confirmed the thermal stabilization and conformational changes that seem to be associated with the binding. The binding constants of ct-DNA-PA complex, in the absence and presence of EMF, have been evaluated to be 6.19 × 104 M-1 and 2.95 × 104 M-1 at 298 K, respectively. In the absence of EMF, the ∆H0 and ∆S0 values that occur in the interaction process of PA with ct-DNA have been measured to be -11.81 kJ.mol-1 and 51.01 J.mol-1K-1, while in the presence of EMF they were observed to be -23.34 kJ.mol-1 and 7.49 J.mol-1K-1, respectively. These numbers indicate the involvement of multiple non-covalent interactions in the binding procedure. In a parallel study, DNA-PA interactions have been monitored by molecular dynamics simulations; their results have demonstrated DNA stability with increasing concentrations of PA, as well as calculated bindings of theoretical ΔG0. Conclusion: The complex formation between PA and ct-DNA has been investigated in the presence and absence of EMF through the multi spectroscopic techniques and MD simulation. These findings have been observed to be parallel to the results of KI and NaCl quenching studies, as well as the competitive displacement with EB and AO. According to thermodynamic parameters, electrostatic interactions stand as the main energy that binds PA to ct-DNA. Regarding the cases that involve the Tm of ct-DNA, EMF has proved to increase the stability of binding between PA and ct-DNA.
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Affiliation(s)
- Atena Sharifi-Rad
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atiye Talebi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Niknaz Nosrati
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Morvarid Medalian
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mahtab Pejhan
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Nazanin Hamzkanloo
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran,Corresponding author: Jamshidkhan Chamani, ,
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Samui S, Biswas S, Muniyappa K, Naskar J. Nano‐Assemblies of a Synthetic Peptide: Illuminating Aggregation Potential, Amyloidogenicity and Cytotoxicity. ChemistrySelect 2021. [DOI: 10.1002/slct.202102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Satyabrata Samui
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Soumi Biswas
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - K. Muniyappa
- Department of Biochemistry Indian Institute of Science Bangalore Karnataka 560 012 India
| | - Jishu Naskar
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
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Shahabadi N, Razlansari M. Insight into the binding mechanism of macrolide antibiotic; erythromycin to calf thymus DNA by multispectroscopic and computational approaches. J Biomol Struct Dyn 2021; 40:6171-6182. [PMID: 33525995 DOI: 10.1080/07391102.2021.1877821] [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: 10/22/2022]
Abstract
In the present study, the interactions between Erythromycin drug and calf thymus deoxyribonucleic acid (ct-DNA) were explored by multi spectroscopic techniques (UV-Visible, fluorescence, circular dichroism spectroscopies), viscosity, molecular docking simulation, and atomic force microscopy (AFM). In addition, the values of binding constant were calculated by the UV-Visible and fluorescence spectroscopy. Competitive fluorescence study with methylene blue (MB), acridine orange (AO), and Hoechst 33258 were indicated that the Erythromycin drug could displace the DNA-bound Hoechst, which displays the strong competition of Erythromycin with Hoechst to interact with the groove binding site of DNA. In addition, the observed complexes in AFM analysis comprise the chains of ct-DNA and Erythromycin with an average size of 314.05 nm. The results of thermodynamic parameter calculations (ΔS° = -332.103 ± 14 J mol-1 K-1 and ΔH° = -115.839 ± 0.02 kJ mol-1) approved the critical role of van der Waals forces and hydrogen bonds in the complexation of Erythromycin-DNA. Fluorescence spectroscopy results demonstrate the existence of a static enhancement mechanism in the interaction of Erythromycin-DNA. According to the obtained results, Erythromycin drug interacts with the major groove of ct-DNA. These consequences were further supported by the molecular docking study, and it could be determined that DNA-Erythromycin docked model was in a rough correlation with our experimental results.Communicated by Ramaswamy H. Sarma.
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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
| | - Mahtab Razlansari
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
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Interaction of synthetic antimicrobial peptides of the Hylin a1 family with models of eukaryotic structures: Zwitterionic membranes and DNA. Biochem Biophys Rep 2020; 24:100827. [PMID: 33195825 PMCID: PMC7644857 DOI: 10.1016/j.bbrep.2020.100827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 11/22/2022] Open
Abstract
Antimicrobial peptides (AMPs) have been appointed as a possible alternative to traditional antibiotics in face of pathogens increasing resistance to conventional drugs. Hylin a1 (IFGAILPLALGALKNLIK), an AMP extracted from the skin secretion of a South American frog, Hypsiboas albopunctatus, was found to show a strong cytotoxicity against bacteria and fungus, but also a considerable hemolytic action. Considering the toxicity of the peptide in eukaryotic cells, this work focuses on investigating the effects of the interaction of the Hylin a1 analogues W6Hya1, D0W6Hya1 and K0W6Hya1 with models of eukaryotic structures, namely zwitterionic liposomes of dipalmitoyl phosphatidylcholine (DPPC) and calf-thymus DNA (CT DNA). Through intrinsic Trp fluorescence we determined that the peptide affinity for fluid DPPC bilayers follows the decreasing order: D0W6Hya1 (+2) > W6Hya1 (+3) » K0W6Hya1 (+4). Fluorescence data also indicate that the Trp residue in the more positively charged peptide, K0W6Hya1, is less deep in the bilayer than the residue in the other two peptides. This finding is supported by differential scanning calorimetry (DSC) data, which shows that both D0W6Hya1 and W6Hya1 disturb DPPC gel-fluid transition slightly more effectively than K0W6Hya1. DPPC DSC profiles are homogeneously disturbed by the three peptides, probably related to peptide-membrane diffusion. Surprisingly, the peptide that displays the lowest affinity for PC membranes and is located at the more superficial position in the bilayer, K0W6Hya1, is the most efficient in causing formation of pores on the membrane, as attested by carboxyfluorescein leakage assays. The three peptides were found to interact with CT DNA, with a deep penetration of the Trp residue into hydrophobic pockets of the double helix, as indicated by the significant blue shift on the Trp fluorescence, and the displacement of DNA-bound ethidium bromide by the peptides. The experiments of DNA electrophoresis confirm that Hylin peptides bind DNA in a concentration-dependent manner, inducing complete DNA retardation at the relative AMP/plasmid DNA weight ratio of ~17. These findings could help to better understand the AMPs toxic effects on eukaryotic cells, thus contributing to the design of healthier therapeutic agents. AMP Hylin a1 analogues bind to both a model of eukaryotic membrane and DNA. The most cationic peptide has lowest affinity to PC vesicle and shallower binding. Peptide lower bilayer affinity is related to greater vesicle disruption and leakage. •AMP hylin a1 analogues deep penetrate into hydrophobic pockets of CT-DNA double helix.
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Abstract
Islet dysfunction is a hallmark of type 2 diabetes mellitus (T2DM). Compelling evidence suggests that accumulation of islet amyloid in the islets of Langerhans significantly contribute to β-cell dysfunction and diabetes. Emerging evidence implicates a role for cystic fibrosis transmembrane-conductance regulator in the regulation of insulin secretion from pancreatic islets. Impaired first-phase insulin responses and glucose homeostasis have also been reported in cystic fibrosis patients. The transforming growth factor-β protein superfamily is central regulators of pancreatic cell function, and has a key role in pancreas development and pancreatic disease, including diabetes and islet dysfunction. It is also becoming clear that islet inflammation plays a key role in the development of islet dysfunction. Inflammatory changes, including accumulation of macrophages, have been documented in type 2 diabetic islets. Islet dysfunction leads to hyperglycemia and ultimately the development of diabetes. In this review, we describe these risk factors and their associations with islet dysfunction.
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Affiliation(s)
- Fei Hu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
| | - Xiaohui Qiu
- Department of nephrology, Ningbo Medical Center Li Huili Eastern Hospital Affiliated to Ningbo University
| | - Shizhong Bu
- Diabetes Research Center, School of Medicine, Ningbo University, Ningbo, China
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Samui S, Biswas S, Roy K, Deb I, Naskar J. Engineering of Supramolecular β-Sheet and Nontoxic Amyloid Fibrils from Synthetic Oligopeptides Containing γ-Aminobutyric Acid as the N-Terminal Residue. ACS Chem Neurosci 2019; 10:2915-2918. [PMID: 31082196 DOI: 10.1021/acschemneuro.9b00119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Here we demonstrate that three synthetic tripeptides containing conformationally flexible γ-aminobutyric acid (γ-Abu) as the N-terminal residue form supramolecular β-sheet and nanofibrillar aggregates upon self-association in aqueous medium. Congo red and thioflavin T binding study establish that these nanofibrillar aggregates are amyloidogenic in nature. The MTT cell survival assay suggests that these amyloid-like nanofibrillar aggregates are nontoxic toward cultured Neuro 2A cells. Interestingly, none of these tripeptides bear sequence identity with any amyloid forming proteins or peptides; however upon self-association, they form supramolecular β-sheet and amyloid-like nanofibrils those are nontoxic in nature. The results highlight the self-assembling nature of the conformationally flexible peptides in aqueous environment and support the hypothesis that amyloid formation is the intrinsic property of the polypeptide chain. Also the cytotoxicity is not predictive from amyloid fibril formation alone. Such nontoxic amyloid fibrils can be exploited in future to design functional biomaterials for various biomedical applications.
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Affiliation(s)
- Satyabrata Samui
- Department of Biochemistry & Biophysics, University of Kalyani, Nadia, WB 741235, India
| | - Soumi Biswas
- Department of Biochemistry & Biophysics, University of Kalyani, Nadia, WB 741235, India
| | - Kaninika Roy
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Rd., Kolkata, 700019, India
| | - Ishani Deb
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Rd., Kolkata, 700019, India
| | - Jishu Naskar
- Department of Biochemistry & Biophysics, University of Kalyani, Nadia, WB 741235, India
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Shahabadi N, Abbasi AR, Moshtkob A, Shiri F. DNA-binding studies of a new Cu(II) complex containing reverse transcriptase inhibitor and anti-HIV drug zalcitabine. J COORD CHEM 2019. [DOI: 10.1080/00958972.2019.1620216] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
| | - Amir Reza Abbasi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Institute of Nano Science and Nano Technology, Razi University, Kermanshah, Islamic Republic of Iran
| | - Ayda Moshtkob
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
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