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Leilabadi-Asl A, Divsalar A, Zare Karizak A, Fateminasab F, Shityakov S, Eslami Moghadam M, Saboury AA. Unraveling the binding interactions between two Pt(II) complexes of aliphatic glycine derivatives with human serum albumin: A comprehensive computational and multi-spectral investigation. Int J Biol Macromol 2024; 266:131298. [PMID: 38574913 DOI: 10.1016/j.ijbiomac.2024.131298] [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: 01/31/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024]
Abstract
This article delves into the interaction between HSA protein and synthesized platinum complexes, with formula: [Pt(Propyl-NH2)2(Propylglycine)]NO3 and [Pt(Tertpentyl-NH2)2(Tertpentylglycine)]NO3, through a range of methods, including spectroscopic (UV-visible, fluorescence, synchronous fluorescence and CD) analysis and computational modeling (molecular docking and MD simulation). The binding constants, the number of binding sites, and thermodynamic parameters were obtained at 25 to 37 °C. The study found that both complexes could bind with HSA (moderate affinity for Tertpentyl and strong affinity for Propyl derivatives) and occupied one binding site in HSA (validated with, Stern-Volmer, Job-plots, and molecular docking investigations) located in subdomain IIA. The binding mechanisms of both mentioned Pt(II) agents were different, with the Propyl derivative predominantly using van der Waals forces and hydrogen bond interactions with a static quenching mechanism and the Tertpentyl derivative mainly utilizing hydrophobic force with a dynamic quenching mechanism. However, the two ligands affected protein differently; the Tertpentyl complex did not significantly alter the protein structure upon binding, as evidenced by synchronous fluorescence spectroscopy (SFS), CD spectroscopy, and MD analysis. The outcome helps in understanding the binding mechanisms and structural modifications induced by the ligands, which could aid in the innovation of more effective and stable Pt(II)-based drugs.
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Affiliation(s)
- Amineh Leilabadi-Asl
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Adeleh Divsalar
- Department of Cell & Molecular Sciences, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Ashkan Zare Karizak
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Fatemeh Fateminasab
- Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar 47416-95447, Iran
| | - Sergey Shityakov
- ITMO University, Infochemistry Scientific Center, Division of Chemoinformatics, Saint-Petersburg 191002, Russian Federation
| | | | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Shahabadi N, Ghaffari L, Mardani Z, Shiri F. Multi‐Spectroscopic and Theoretical Analyses of Human Serum Albumin Binding to a Water‐Soluble Zinc(II) Complex including β‐Amino Alcohol. ChemistrySelect 2022. [DOI: 10.1002/slct.202200645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry Faculty of Chemistry Razi University Kermanshah Iran
| | - Lida Ghaffari
- Department of Inorganic Chemistry Faculty of Chemistry Razi University Kermanshah Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry Faculty of Chemistry Urmia University Urmia Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry Faculty of Chemistry Razi University Kermanshah Iran
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Shahabadi N, Ghaffari L, Mardani Z, Shiri F. Experimental and Molecular Docking Studies on the Interaction of a Water-Soluble Pd(II) Complex Containing β-Amino Alcohol with Calf Thymus DNA. Biol Trace Elem Res 2022; 200:1988-2000. [PMID: 34218426 DOI: 10.1007/s12011-021-02803-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/18/2021] [Indexed: 02/03/2023]
Abstract
The interaction of water-soluble and fluorescent [Pd (HEAC) Cl2] complex, in which HEAC is 2-((2-((2-hydroxyethyl)amino)ethyl)amino) cyclohexanol, with calf thymus DNA (ct-DNA) has been studied. This study was performed using electronic absorption and fluorescence emission spectroscopies, cyclic voltammetry and circular dichroism analyses, dynamic viscosity measurements, and molecular docking theory. From hypochromic effect observed in ct-DNA absorption spectra, it was found that the Pd(II) complex could form a conjugate with ct-DNA strands through the groove binding mode. The Kb values obtained from fluorescence measurements clearly assert the Pd(II) complex affinity to ct-DNA. The fluorescence quenching of the DNA-Hoechst compound following the successive additions of the Pd(II) complex to the solution revealed that the Pd(II) complex is located in the ct-DNA grooves, and Hoechst molecules have been released into solution; moreover, the resulting measurements from relative viscosity authenticate the Pd(II) complex binding to the grooves. Negative quantities of thermodynamic parameters imply that the Pd(II) complex binds to ct-DNA mainly by the hydrogen bonds and van der Waals forces; also, the Gibbs-free energy changes show the exothermic and spontaneous formation of the Pd(II) complex-DNA system. The electrochemical behavior of the Pd(II) complex in the attendance of ct-DNA was investigated using the cyclic voltammetry method (CV). Several quasi-reversible redox waves were observed along with increasing the anodic/cathodic peak currents, as well as a shift in anodic/cathodic peak potentials. Circular dichroism (CD) observations suggested that the Pd(II)-DNA interaction could alter ct-DNA conformation. The results of molecular modeling confirmed that groove mechanism is followed by the Pd(II) complex to interact with ct-DNA.
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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.
| | - Lida Ghaffari
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
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Spectroscopic (FT-IR, Raman) analysis and computational study on conformational geometry, AIM and biological activity of cephalexin from DFT and molecular docking approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Liao T, Zhang Y, Huang X, Jiang Z, Tuo X. Multi-spectroscopic and molecular docking studies of human serum albumin interactions with sulfametoxydiazine and sulfamonomethoxine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119000. [PMID: 33032113 DOI: 10.1016/j.saa.2020.119000] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/24/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Sulfonamides are a kind of antibiotics which have been widely used as feed additives for livestock and poultry. However, sulfa drugs have raised worldwide concerns because of their adverse impact on human health. In this study, two sulfonamides, sulfametoxydiazine (SMD) and sulfamonomethoxine (SMM), were selected to explore the binding modes with human serum albumin (HSA). The spectroscopic approaches revealed that SMD or SMM could spontaneously enter into the binding site I of HSA through hydrogen bond interactions and van der Waals forces, and that SMD exhibited much stronger binding affinity toward HSA than SMM at different temperatures (p < 0.01, n = 3). The binding constants for SMD-HSA and SMM-HSA were determined to be (8.297 ± 0.010) × 104 L·mol-1 and (1.178 ± 0.008) × 104 L·mol-1 at 298 K, respectively. The interaction of SMD or SMM to HSA induced microenvironmental and conformational changes in HSA, where SMD had a greater effect on the α-helix content of HSA. Results from molecular docking implied that the amino acid residues of HSA, such as Arg222, Ala291 and Leu238, played key roles in the sulfonamide-HSA binding process. Meanwhile, hydrogen bonds might be a key factor contributing to the binding affinity of sulfa drugs and HSA. Additionally, the combined use of SMD and SMM led to an obvious variation in Ka values of binary systems (p < 0.01, n = 3). These findings might be helpful to understand the biological effects of sulfonamides in humans.
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Affiliation(s)
- Tancong Liao
- School of Life Sciences, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Yuai Zhang
- NanChang BO ZE KANG Pharmaceutical Technology Co., LTD, Nanchang 330000, Jiangxi, China
| | - Xiaojian Huang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Zheng Jiang
- School of Pharmacy, Nanchang University, Nanchang 330031, Jiangxi, China
| | - Xun Tuo
- Basic Chemistry Experiment Center, College of Chemistry, Nanchang University, Nanchang 330031, Jiangxi, China.
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Pereira AKDS, Manzano CM, Nakahata DH, Clavijo JCT, Pereira DH, Lustri WR, Corbi PP. Synthesis, crystal structures, DFT studies, antibacterial assays and interaction assessments with biomolecules of new platinum(ii) complexes with adamantane derivatives. NEW J CHEM 2020. [DOI: 10.1039/d0nj02009e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Synthesis, crystal structures and antibacterial activities of new Pt(ii) complexes with adamantane derivatives are presented in this article.
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Affiliation(s)
| | | | | | | | | | - Wilton Rogério Lustri
- Department of Biological and Health Sciences
- University of Araraquara
- UNIARA
- São Paulo
- Brazil
| | - Pedro Paulo Corbi
- Institute of Chemistry
- University of Campinas – UNICAMP
- 13083-970 Campinas
- Brazil
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Shahabadi N, Momeni BZ, Zendehcheshm S. Studies on the Interaction of [SnMe 2Cl 2(bu 2bpy)] Complex with ct-DNA Using Multispectroscopic, Atomic Force Microscopy (AFM) and Molecular Docking. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:157-182. [PMID: 31044667 DOI: 10.1080/15257770.2018.1506885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The interaction of SnMe2Cl2(bu2bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV-Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe2Cl2(bu2bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859 nm were observed by using AFM for Sn(IV) Complex-DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO2 group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe2Cl2(bu2bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA-complex mixture confirmed the experimental results.
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Affiliation(s)
- Nahid Shahabadi
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Badri Z Momeni
- c Department of Chemistry , K. N. Toosi University of Technology , Tehran , Iran
| | - Saba Zendehcheshm
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran
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