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Vinod SM, Murugan Sreedevi S, Krishnan A, Ravichandran K, Karthikeyan P, Kotteswaran B, Rajendran K. Complexity of the Role of Various Site-Specific and Selective Sudlow Binding Site Drugs in the Energetics and Stability of the Acridinedione Dye-Bovine Serum Albumin Complex: A Molecular Docking Approach. ACS OMEGA 2023; 8:5634-5654. [PMID: 36816669 PMCID: PMC9933201 DOI: 10.1021/acsomega.2c07111] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Molecular docking (Mol.Doc) techniques were employed to ascertain the binding affinity of two resorcinol-based acridinedione dyes (ADR1 and ADR2) with the widely studied globular protein Bovine Serum Albumin (BSA) in the presence of site-selective binding drugs by Autodock Vina 4.2 software. Docking of various feasible conformers of ADR1 dye with BSA was found to be energetically more favored than ADR2 dye, even though both these dyes differ in the 9th position of the basic dye structure. Analysis of dyes with BSA establishes the location of dye in all of the binding sites of BSA, predominantly through conventional and nonconventional hydrogen-bonding (HB) interactions. The coexistence of hydrophobic interactions resulted in the stability of various conformers generated. The introduction of site I and site II (Sudlow site binding drugs) into ADR1-BSA and ADR2-BSA complexes effectively destabilizes the dye-protein complex; however, the drugs do not displace ADR dyes completely from their selective binding domains. Site II binding drugs effectively destabilize the binding ability of the dye-protein complex rather than site I drugs. However, docking of site I drug 3-carboxyl-4-methyl-5-propyl-2-furanpropanic acid (CMPF) largely destabilizes the ADR1-protein complex, whereas indomethacin (INDO) enhances the binding affinity of the ADR2-protein complex. Interestingly, simultaneous docking of ADR dyes to the BSA-drug complex results in larger stability of the protein-drug complex through HB interactions rather than hydrophobic interactions. Both ADR1 and ADR2 dyes predominantly occupy the Sudlow binding sites of BSA, and the introduction of either site I or site II binding drugs does not displace the dye efficiently from the corresponding binding sites, rather the drugs are effectively displaced toward other binding domains apart from their specific site-binding domains of BSA. Through Mol.Doc techniques, we authenticate that the interactions in host-guest complex systems involving competing ligands are established in depth, wherein the dye as well as the amino acid (AA) moieties in BSA act as both HB donor and acceptor sites apart from several hydrophobic interactions coexisting toward the stability.
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Affiliation(s)
- Seba Merin Vinod
- Department
of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R. Periyar
Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Sangeetha Murugan Sreedevi
- Department
of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R. Periyar
Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Anju Krishnan
- Department
of Chemistry, Sathyabama Institute of Science
and Technology, Kamaraj
Nagar, Semmancheri, Chennai 600119, Tamil Nadu, India
| | - Keerthiga Ravichandran
- Department
of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R. Periyar
Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Pradeep Karthikeyan
- Department
of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R. Periyar
Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Bharath Kotteswaran
- Department
of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R. Periyar
Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
| | - Kumaran Rajendran
- Department
of Chemistry, Dwaraka Doss Goverdhan Doss
Vaishnav College (Autonomous) (Affiliated to University of Madras), 833, Gokul Bagh, E.V.R. Periyar
Road, Arumbakkam, Chennai 600106, Tamil Nadu, India
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Fluorescent properties of amphi-PIC J-aggregates in the complexes with bovine serum albumin. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Turn-on Fluorescence of Davydov-Split Aggregate Particles for Protein Detection. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Pronkin PG, Tatikolov AS. Meso-aryl-substituted thiacarbocyanine dyes as spectral-fluorescent probes for DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120744. [PMID: 34929626 DOI: 10.1016/j.saa.2021.120744] [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: 10/05/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The noncovalent interaction of meso-aryl-substituted thiacarbocyanine dyes I and II with dsDNA and ssDNA in aqueous solutions has been studied by spectral-fluorescent methods. Complexation with DNA is accompanied by both aggregation of the dyes and the formation of monomeric strongly fluorescent complexes. Experiments on molecular docking of dyes I and II with dsDNA confirm the previous assumption about the possibility of the formation of complexes of different types: intercalation between base pairs and in the grooves of the double helix of the biopolymer. The possibility of intercalation of the dyes in the complex is confirmed by experiments on thermal dissociation of dsDNA in the presence of dyes I and II, as well as experiments on the interaction of the dyes with ssDNA. An increase in the melting temperatures Tm of dsDNA is obtained in the presence of I and II, similar to that observed for the classical intercalator ethidium bromide. The limits of detection and quantification of DNA, which are important for the use of the dyes as probes for DNA, have been determined. The primary photochemical processes of the dyes in complexes with ssDNA were studied by flash photolysis technique. Complexation with ssDNA hinders photoisomerization and creates favorable conditions for the dye triplet state formation. The decay kinetics of the triplet state of the dyes were monoexponential. The rate constant of quenching of the triplet state by air oxygen was estimated for dye I complexed with ssDNA and was found to be less than the diffusion-controlled limit. This is probably a consequence of the shielding effect of the complex on the triplet quenching process.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
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Zhang HX, Xia QH, Zhou D. Effect of carbamylation on the molecular recognition action of amino benzothiazole by carrier protein. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117595. [PMID: 31675655 DOI: 10.1016/j.saa.2019.117595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/12/2019] [Accepted: 10/02/2019] [Indexed: 05/23/2023]
Abstract
Increasing benzothiazole derivatives containing amino or N-acyl structures in position 2 have been largely developed as pesticides and medicines. However, the structure-function relationship of 2-substituted benzothiazole derivatives has seldom been illustrated from the perspective of their albumin-binding nature. Herein, to probe the influence of carbamylation on the albumin-binding nature of benzothiazole derivatives, formyl group was introduced to the amine group of 2-amino benzothiazole (ABT) to yield a novel modified ABT (MABT). Their protein-binding properties were systematically deciphered by spectroscopy, molecular modeling and density functional theory (DFT) calculations. The interaction mechanisms, recognition thermodynamics and binding geometry were investigated and compared. The structural alteration of human serum albumin was explored using synchronous fluorescence emission and circular dichroism spectrum technologies. Based on experimental results, the structures of protein complex with MABT and ABT were revealed by molecular docking method. The differences in energy transfer efficiency and molecular orientation of ABT and MABT in new complexes were tentatively explained by DFT calculations. The work was expected to help to understand the impact of different substituents on the bioactivity of benzothiazole derivatives and guide for structural designs of new compounds.
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Affiliation(s)
- Hua-Xin Zhang
- Ministry-of-Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan, 430062, PR China; Hubei Key Laboratory of Drug Synthesis and Optimization, Jingchu University of Technology, Jingmen, 448000, PR China.
| | - Qing-Hua Xia
- Ministry-of-Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan, 430062, PR China
| | - Dan Zhou
- Ministry-of-Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan, 430062, PR China.
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