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.

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.

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.

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.

Electrochemical Investigation and Molecular Docking Techniques on the Interaction of Acridinedione Dyes with Water-Soluble Nonfluorophoric Simple Amino Acids.

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.

A fluorescence approach on the investigation of urea derivatives interaction with a non-PET based acridinedione dye-beta Cyclodextrin (ß-CD) complex in water: Hydrogen-bonding interaction or hydrophobic influences or combined effect?

Photophysical studies of resorcinol based acridinedione dyes with beta Cyclodextrin (ß-CD) in the presence of urea (U) and tetramethylurea (TMU) were carried out in water. A marked variation in the absorption spectra of dye-ß-CD complex was found to be more significant in the case of U rather in TMU. Interestingly, the role of urea on the excited state behavior of dye-ß-CD complex is found to be entirely different from that of TMU. The formation of urea-water hydrogen-bonding self assemblies and creation of microspheres of varying environment results in an effective displacement of dye from the hydrophobic nanocavity of ß-CD. On the contrary, the dye prefers a more confined hydrophobic micro environment in the presence of TMU. The nature of urea derivative, hydrogen-bonding of urea-water assemblies and hydrophobic influences of methyl moieties in urea molecular framework governs the stability and also the dissociation of dye-ß-CD complex. The displacement of dye from the environment of the sugar molecule by urea derivatives is established from fluorescence studies wherein the variation in the spectral behavior of non-PET based dye-ß-CD complex is found to be entirely different from that of PET dye. Both hydrogen-bonding along with hydrophobic interactions influences the excited state properties of the both PET and non-PET based acridinedione dyes are elucidated through fluorescence spectral studies. The extent of binding and the microenvironment of the dye in the presence of ß-CD and urea are established through molecular docking and fluorescence anisotropy studies.

Competitive hydrogen bonding influences of fluorophore- urea-adenine system in water: Photophysical and photochemical approaches.

Photophysical and photochemical investigation of photoinduced electron transfer (PET)-based acridinedione dye (ADR1) with urea in the presence of a nitrogenous base (adenine) were carried out in water. Urea suppresses the PET resulting in a fluorescence enhancement and the extent of binding is correlated and governed by the number of urea molecules surrounding the close vicinity of dye. On the contrary, adenine forms a true 1:2 complex with dye. Presence of adenine in dye-urea microenvironment results in the displacement of dye from the vicinity of urea molecules. The stability of dye-urea network in the presence of adenine reveals that the microenvironment of dye is governed and influenced by both urea and adenine. Introduction of adenine to dye-urea results in the formation of several hydrogen bonding assemblies that are competitive and influences the excited state characteristics of ADR1 dye. The micro assemblies comprise dye-urea (DU), dye-adenine (DA), urea-adenine (UA), urea-water (UW), urea-urea (UU), and adenine-water (AW) framework and the existence of several competitive hydrogen bonding results in a large variation in fluorescence properties of ADR1 dye. The presence of several assemblies also signifies that no confined phase selectively of DU or DA assemblies exist in any stoichiometric proportion in the aqueous phase. The binding constant, the variation in the fluorescence lifetime and its relative amplitude of DA in the presence of urea authenticate that the binding nature of dye-urea-adenine (DUA) is dependent on the several hydrogen bonding assemblies that coexist at any concentration. The extent of hydrogen bonding of DA is found to be entirely different from that of urea. Further, urea resulted in changes in the transient absorption peak of dye with a large variation in lifetime and shift of the transient absorption peaks. Fluorescence spectral techniques are used as an efficient tool in elucidating the binding nature of DU framework in the presence of non-fluorescent hydrogen-bonding solute like adenine.