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Grabowska O, Samsonov SA, Kogut-Günthel MM, Żamojć K, Wyrzykowski D. Elucidation of binding mechanisms of bovine serum albumin and 1-alkylsulfonates with different hydrophobic chain lengths. Int J Biol Macromol 2024; 266:131134. [PMID: 38537848 DOI: 10.1016/j.ijbiomac.2024.131134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
In this article, the binding interactions between bovine serum albumin (BSA) and three 1-alkylsulfonates, namely sodium 1-dodecanesulfonate, sodium 1-decanesulfonate, and sodium 1-octanesulfonate, have been thoroughly investigated. The study employed various experimental techniques such as isothermal titration calorimetry (ITC), steady-state fluorescence spectroscopy (SF), circular dichroism spectroscopy (CD), and molecular dynamics-based simulations. The objective was to understand the influence of the alkyl chain length of the investigated ligands on several aspects, including the strength of the interaction, the stoichiometry of the resulting complexes, the number of BSA binding sites, and the underlying mechanisms of binding. Notably, the study also demonstrated that sodium dodecyl sulfate (S12S) can serve as an effective site marker for BSA when studying ligands with similar structural and topological features. These findings may have significant implications for enhancing our understanding of the interactions between small amphiphilic molecules and proteins.
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Affiliation(s)
- Ola Grabowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Sergey A Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Małgorzata M Kogut-Günthel
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; Leibniz-Institut für Lebensmittel-Systembiologie an der Technischen Universität München, 85354 Freising, Germany
| | - Krzysztof Żamojć
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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Vinod SM, Murugan Sreedevi S, Krishnan A, Perumal T, Chinnadurai R, Rajendran K. Interaction of an Aldose Sugar with Photoinduced Electron Transfer (PET) and Non-PET Based Acridinedione Dyes in Water: Hydrogen-bonding Evidences from Fluorescence Spectral Techniques Assisted by Molecular Docking Approach. J Fluoresc 2023; 33:471-486. [PMID: 36445509 DOI: 10.1007/s10895-022-03062-6] [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: 07/08/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022]
Abstract
Fluorescence spectral techniques aided by molecular docking (Mol.Doc) approach were employed in probing the molecular interactions existing between D-glucose and resorcinol based acridinedione (ADR) dyes. ADR dyes has been classified into PET and non-PET dyes based on the substitution in the 9th position of acridinedione ring structure. Addition of glucose to PET dye (ADR1) resulted in a decrease in the absorbance whereas to that of ADR2 dye (non-PET character in aqueous medium) resulted in a significant increase in the absorbance. The formation of an isosbestic point reveals the existence of a ground state interaction existing between the dye and sugar molecule. Addition of glucose to PET dye resulted in a drastic increase in the fluorescent enhancement (FE) and subsequent addition resulted in a marked decrease in the fluorescent intensity with no apparent shift of emission maximum. Interestingly, neither characteristic shift nor variation in emission intensity was observed in the case of ADR2 dye. Fluorescence lifetime studies of ADR1 dye in the presence of glucose illustrate the existence of multiple distinguishable micro environments of dye. Mol.Doc studies authenticate the co-existence of hydrogen bonding (HB) and hydrophobic interaction wherein the dye and sugar molecule acts as HB donor and acceptor resulting in a stable conformer. These conformers are governed predominantly by HB interactions. The nature of interaction of a simple sugar with ADR dyes are explored in depth by fluorescent techniques in coordination with docking studies is imparted in the present study.
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Affiliation(s)
- Seba Merin Vinod
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India
| | - Sangeetha Murugan Sreedevi
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India
| | - Anju Krishnan
- Department of Chemistry, Sathyabama Institute of Science and Technology, Tamil Nadu, Kamaraj Nagar, Semmancheri, Chennai, 600119, India
| | - Tamizhdurai Perumal
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India
| | - Raghupathi Chinnadurai
- Department of Chemistry, Sriram College of Arts and Science, Tamil Nadu, Perumalpattu, Tiruvallur, 602024, India
| | - Kumaran Rajendran
- Department of Chemistry, Dwaraka Doss Goverdhan Doss Vaishnav College (Autonomous)(University of Madras)Tamil Nadu, Gokul Bagh, E.V.R.Periyar Road, 833, Arumbakkam, Chennai, India.
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Şuekinci Yılmaz A, Uluçam G. Novel N-benzyl-2-oxo-1,2-dihydrofuro [3,4-d]pyrimidine-3(4H)-carboxamide as anticancer agent: Synthesis, drug-likeness, ADMET profile, DFT and molecular modelling against EGFR target. Heliyon 2023; 9:e12948. [PMID: 36711281 PMCID: PMC9876965 DOI: 10.1016/j.heliyon.2023.e12948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
A novel compound N-benzyl-2-oxo-1,2-dihydrofuro [3,4-d]pyrimidine-3(4H)-carboxamide (DHFP) was synthesized by addition, rearrangement, and intramolecular cyclization reactions. The three-dimensional geometry of DHFP has been determined by density functional theory calculations in the gas phase. Thus, the geometrical properties of DHFP such as the bond lengths, bond angles, and dihedral bond angles have been determined in the optimized molecular configuration. Also, the HOMO-LUMO energies were calculated. The charge distribution of the DHFP has been calculated by Natural Population Analysis (NPA) approach. NMR and FTIR spectra were calculated and compared with their experimental corresponding to confirm the synthesis of the DHFP. The anticancer activities of the DHFP were also determined on human colon cancer (HT29) and prostate cancer (DU145) cell lines. Molecular docking studies of the DHFP with EGFR tyrosine kinase, which is responsible for cancer cell proliferation and growth, were performed and it was observed that docking interaction took place. The DHFP has the potential to be a drug, as it is determined that DHFP obeys Lipinski's five rules, can cross the blood-brain barrier, and can be rapidly absorbed from the gastrointestinal wall.
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Affiliation(s)
- Ayşen Şuekinci Yılmaz
- Corresponding author. Chemistry Department, Faculty of Science, Trakya University, 22030, Edirne, Turkey.
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Sreedevi Sangeetha M, Merin Vinod S, Anju K, Tamizhdurai P, Raghupathi C, Kumaran R. Photophysical and molecular docking approach on the interaction of water-soluble simple keto sugar with Acridinedione dyes. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Ramachandran TS, Gunasekaran S, Murugan Sreedevi S, Vinod SM, Rajendran K, Perumal T, Amer M. A, P.-S. G. Comparative studies on biophysical interactions between 4-dicyanomethylene-2,6-dimethyl-4H-pyran (DDP) with bovine serum albumin (BSA) and human serum albumin (HSA) via photophysical approaches and molecular docking techniques. JOURNAL OF SAUDI CHEMICAL SOCIETY 2021. [DOI: 10.1016/j.jscs.2021.101364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Anupurath S, Rajaraman V, Gunasekaran S, Krishnan A, Sreedevi SM, Vinod SM, Dakshinamoorthi BM, Rajendran K. Electrochemical Investigation and Molecular Docking Techniques on the Interaction of Acridinedione Dyes with Water-Soluble Nonfluorophoric Simple Amino Acids. ACS OMEGA 2021; 6:30932-30941. [PMID: 34841136 PMCID: PMC8613813 DOI: 10.1021/acsomega.1c03172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Electrochemical studies of resorcinol-based acridinedione (AD) dyes with nonfluorophoric simple amino acids, glycine, alanine, and valine, were carried out in water. AD probes are classified into photoinduced electron transfer (PET) and non-PET-based dyes, wherein the electrochemical properties and photophysical and photochemical behavior vary significantly based on the nature of substituent groups and the nature of the solute. The oxidation potential of PET dye (ADR1) to that of non-PET-based dye (ADR2) differs significantly such that the addition of amino acids results in a shift of the oxidation peak to a less positive potential and the reduction peak to a lesser negative potential. The extent of shift of oxidation and reduction potential in PET dye is more pronounced than that of non-PET dye on the addition of valine rather than glycine. The variation in the shift is attributed to the presence of an electron-donating moiety (OCH3) group in the ninth position of ADR1 dye. Consequently, the quenching of fluorescence is observed in ADR2 with non fluorophoric amino acids that are authenticated by the shift of the anodic and cathodic peaks toward a lesser positive potential. Molecular docking (MD) studies of PET and non-PET dye with amino acids portray that neither hydrophobic interactions nor electrostatic or weak interactions such as van der Waals and pi-pi interactions govern the electrochemical nature of dye on the addition of amino acids. Furthermore, the formation of a conventional hydrogen bond between dye and amino acid is established from MD studies. The existence of dye-water-amino acid competitive hydrogen-bonding interactions is presumably well-oriented throughout the aqueous phase as observed through photophysical studies which support our electrochemical investigation.
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Affiliation(s)
- Sumita Anupurath
- Department
of Chemistry, Anna Adarsh College for Women, University of Madras, Chennai, Tamil Nadu 600 040, India
| | - Vasanthi Rajaraman
- P.G
and Research Department of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous), University
of Madras, Chennai, Tamil Nadu 600 106, India
| | - Shoba Gunasekaran
- Department
of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav (Autonomous), University of Madras, Chennai, Tamil Nadu 600
106, India
| | - Anju Krishnan
- Department
of Chemistry, Anna Adarsh College for Women, University of Madras, Chennai, Tamil Nadu 600 040, India
| | - Sangeetha Murugan Sreedevi
- P.G
and Research Department of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous), University
of Madras, Chennai, Tamil Nadu 600 106, India
| | - Seba Merin Vinod
- P.G
and Research Department of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous), University
of Madras, Chennai, Tamil Nadu 600 106, India
| | | | - Kumaran Rajendran
- Department
of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav (Autonomous), University of Madras, Chennai, Tamil Nadu 600
106, India
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