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Binding interaction of a novel fluorophore with serum albumins: steady state fluorescence perturbation and molecular modeling analysis.

Pal U, Pramanik SK, Bhattacharya B, Banerji B, Maiti NC - Springerplus (2015)

Bottom Line: The fluorescence yield of the compound substantially increased inside hydrophobic protein surface and ~30 nm decrease in Stokes' shift, compared to aqueous solution, was observed.Thus, the molecule appears as a new fluorescence probe to report the nature of its binding site in terms of increased fluorescence quantum yield and decreased Stokes' shift.Further it could be useful to detect and study the drug binding site of specific protein of interest.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal India.

ABSTRACT
Fluorescence emission and anisotropy are widely used to measure the binding parameters and kinetic behavior of reactions that cause a change in the rotational time of a fluorescent molecule. We report here fluorescence emission and anisotropy behavior of a newly synthesized novel naphthalene base fluorophore (methyl 3-[(6-{[2-(tert-butoxy)-2-oxoethyl] (4-methoxyphenyl)amino}naphthalen-2-yl)formamido]propanoate) in several solution conditions including its binding to human and bovine serum albumin proteins both in their native and denatured states. The fluorescence yield of the compound substantially increased inside hydrophobic protein surface and ~30 nm decrease in Stokes' shift, compared to aqueous solution, was observed. Shift in fluorescence excitation peak position from the absorption peak of the molecule was ~8 nm in protein solution. This indicated possible alteration of excited state geometry of the compound by the globular fold of albumins. In addition, we measured the steady state fluorescence anisotropy of the molecule to evaluate several thermodynamic parameters and the results suggested the binding was energetically favorable. The measured ΔG° was ~-30 kJ mol(-1) and the derived dissociation constant was ~10(-6) M. The molecular docking analysis further highlighted the nonspecific association of the compound with the proteins and hydrophobic forces may have a significant role in the binding processes. Under the denatured condition of the protein, the compound lost its binding efficacy and reduction in fluorescence intensity was observed. Thus, the molecule appears as a new fluorescence probe to report the nature of its binding site in terms of increased fluorescence quantum yield and decreased Stokes' shift. It can also report the changes in the binding site due to global change in protein structure such as unfolding/misfolding often linked to several human disorder. Further it could be useful to detect and study the drug binding site of specific protein of interest.

No MeSH data available.


Related in: MedlinePlus

Interaction of compound 5 with serum albumins as obtained from molecular docking experiments. a Best binding conformation of compound 5 with BSA and the close up view. b Best binding conformations of compound 5 with HSA; it is also shown in close up. AutoDock Vina generated complexes are depicted here. Proteins are shown in ribbon diagram and the ligands in stick model. The three domains of serum albumin are marked with I–III. Standard color representation is used to denote the elements, H, N and O in the ligand
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Fig6: Interaction of compound 5 with serum albumins as obtained from molecular docking experiments. a Best binding conformation of compound 5 with BSA and the close up view. b Best binding conformations of compound 5 with HSA; it is also shown in close up. AutoDock Vina generated complexes are depicted here. Proteins are shown in ribbon diagram and the ligands in stick model. The three domains of serum albumin are marked with I–III. Standard color representation is used to denote the elements, H, N and O in the ligand

Mentions: In silico molecular docking calculation shows that the interactions of the compound with serum albumins are thermodynamically favorable (Table 4). The binding free energies computed by AutoDock Vina and SwissDock are very similar to that of the experimentally obtained values (Table 2). Molecular docking also provides the insight into the most favorable binding site for these compounds on the serum albumins. The lowest energy complexes obtained by the three different algorithms consistently showed that the binding sites for compound 5 lay in the groove between domain I and domain III of BSA, whereas it was within the domain I in case of HSA (Fig. 6, Additional file 1: Figure S5). This may, in part, explain the enthalpy driven nature of binding with HSA and the entropy driven binding with BSA (Table 2). Moreover, the non-specific nature of the binding is apparent from the lack of clustering in the AutoDock 4.2 results (Additional file 1: Figure S6). We have shown in earlier works that the low energy high frequency clusters in the AutoDock 4.2 output signifies specificity in the binding interactions (Alam et al. 2012; Rudra et al. 2012; Bhowmik et al. 2013). Serum albumin with its many hydrophobic binding pockets acts like a universal receptor for almost all drug molecules. Binding to serum albumin is generally non-specific in nature and driven by mainly hydrophobic interactions, which is evident in the molecular docking results as well (Additional file 1: Figures S7, S8).Table 4


Binding interaction of a novel fluorophore with serum albumins: steady state fluorescence perturbation and molecular modeling analysis.

Pal U, Pramanik SK, Bhattacharya B, Banerji B, Maiti NC - Springerplus (2015)

Interaction of compound 5 with serum albumins as obtained from molecular docking experiments. a Best binding conformation of compound 5 with BSA and the close up view. b Best binding conformations of compound 5 with HSA; it is also shown in close up. AutoDock Vina generated complexes are depicted here. Proteins are shown in ribbon diagram and the ligands in stick model. The three domains of serum albumin are marked with I–III. Standard color representation is used to denote the elements, H, N and O in the ligand
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4582037&req=5

Fig6: Interaction of compound 5 with serum albumins as obtained from molecular docking experiments. a Best binding conformation of compound 5 with BSA and the close up view. b Best binding conformations of compound 5 with HSA; it is also shown in close up. AutoDock Vina generated complexes are depicted here. Proteins are shown in ribbon diagram and the ligands in stick model. The three domains of serum albumin are marked with I–III. Standard color representation is used to denote the elements, H, N and O in the ligand
Mentions: In silico molecular docking calculation shows that the interactions of the compound with serum albumins are thermodynamically favorable (Table 4). The binding free energies computed by AutoDock Vina and SwissDock are very similar to that of the experimentally obtained values (Table 2). Molecular docking also provides the insight into the most favorable binding site for these compounds on the serum albumins. The lowest energy complexes obtained by the three different algorithms consistently showed that the binding sites for compound 5 lay in the groove between domain I and domain III of BSA, whereas it was within the domain I in case of HSA (Fig. 6, Additional file 1: Figure S5). This may, in part, explain the enthalpy driven nature of binding with HSA and the entropy driven binding with BSA (Table 2). Moreover, the non-specific nature of the binding is apparent from the lack of clustering in the AutoDock 4.2 results (Additional file 1: Figure S6). We have shown in earlier works that the low energy high frequency clusters in the AutoDock 4.2 output signifies specificity in the binding interactions (Alam et al. 2012; Rudra et al. 2012; Bhowmik et al. 2013). Serum albumin with its many hydrophobic binding pockets acts like a universal receptor for almost all drug molecules. Binding to serum albumin is generally non-specific in nature and driven by mainly hydrophobic interactions, which is evident in the molecular docking results as well (Additional file 1: Figures S7, S8).Table 4

Bottom Line: The fluorescence yield of the compound substantially increased inside hydrophobic protein surface and ~30 nm decrease in Stokes' shift, compared to aqueous solution, was observed.Thus, the molecule appears as a new fluorescence probe to report the nature of its binding site in terms of increased fluorescence quantum yield and decreased Stokes' shift.Further it could be useful to detect and study the drug binding site of specific protein of interest.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal India.

ABSTRACT
Fluorescence emission and anisotropy are widely used to measure the binding parameters and kinetic behavior of reactions that cause a change in the rotational time of a fluorescent molecule. We report here fluorescence emission and anisotropy behavior of a newly synthesized novel naphthalene base fluorophore (methyl 3-[(6-{[2-(tert-butoxy)-2-oxoethyl] (4-methoxyphenyl)amino}naphthalen-2-yl)formamido]propanoate) in several solution conditions including its binding to human and bovine serum albumin proteins both in their native and denatured states. The fluorescence yield of the compound substantially increased inside hydrophobic protein surface and ~30 nm decrease in Stokes' shift, compared to aqueous solution, was observed. Shift in fluorescence excitation peak position from the absorption peak of the molecule was ~8 nm in protein solution. This indicated possible alteration of excited state geometry of the compound by the globular fold of albumins. In addition, we measured the steady state fluorescence anisotropy of the molecule to evaluate several thermodynamic parameters and the results suggested the binding was energetically favorable. The measured ΔG° was ~-30 kJ mol(-1) and the derived dissociation constant was ~10(-6) M. The molecular docking analysis further highlighted the nonspecific association of the compound with the proteins and hydrophobic forces may have a significant role in the binding processes. Under the denatured condition of the protein, the compound lost its binding efficacy and reduction in fluorescence intensity was observed. Thus, the molecule appears as a new fluorescence probe to report the nature of its binding site in terms of increased fluorescence quantum yield and decreased Stokes' shift. It can also report the changes in the binding site due to global change in protein structure such as unfolding/misfolding often linked to several human disorder. Further it could be useful to detect and study the drug binding site of specific protein of interest.

No MeSH data available.


Related in: MedlinePlus