Comparative study of the interaction of some meso-substituted anionic cyanine dyes with human serum albumin

Photonics of Some Monomethine Cyanine Dyes in Solutions and in Complexes with Biomolecules

In search of new probes for biomolecules, the spectral fluorescent study of four monomethine cyanine dyes (MCD), both unsymmetrical and symmetrical, has been carried out in different organic solvents, in aqueous buffer solutions, and in the presence of DNA and HSA. The complexation of MCD with biomacromolecules leads to a steep growth of the fluorescence intensity. Complexes of MCD with dsDNA and HSA of various types were modeled in silico by molecular docking. Experiments on thermal dissociation of dsDNA in the presence of MCD showed the formation of intercalative complexes of MCD with DNA. Quenching of intrinsic fluorescence of HSA by MCD occurred with rate constants much higher than the diffusion limit, that is, in dye-HSA complexes. Effective constants of MCD complexation with the biomacromolecules were estimated. MCD 1 has the best characteristics as a possible fluorescent probe for dsDNA and can serve as a sensitive and selective probe for dsDNA in the presence of HSA. Photochemical properties of MCD complexed with DNA have been also studied. An increase in the quantum yield of the triplet states of MCD in complexes with DNA has been found, which may be important for using these dyes as potential candidates in photodynamic therapy.

Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules

Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.

Molecular Docking of Cyanine and Squarylium Dyes with NSP15 Endoribonuclease of the SARS-CoV-2 Coronavirus

The ongoing spread of the COVID-19 coronavirus infection requires us to find new tools and methods for detecting and studying the infection and preventing morbidity (new analytical procedures and tests). With the aim of developing probes for the detection of SARS-CoV-2 coronavirus by modeling in silico (molecular docking), the noncovalent binding of cyanine and squarylium dyes with different molecular charges and different types of heterocyclic residues and substituents (42 compounds in total) with different variants of the NSP15 endoribonuclease of the SARS-CoV-2 coronavirus (COVID-19) of the original (wild) type and mutant types is studied. The interaction energies and spatial configurations of the dye molecules in complexes with NSP15 are determined. Some dyes with negative values of the total energy of the complex E_tot are promising for further practical study as probes for coronavirus.

Meso-aryl-substituted thiacarbocyanine dyes as spectral-fluorescent probes for DNA

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 T_m 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.

Development of a human serum albumin structure-based fluorescent probe for bioimaging in living cells

Forming a stable complex is a prerequisite for intramolecular charge transfer (ICT) probe to recognize proteins. Herein, a human serum albumin (HSA) structure-based fluorescent probe DNPM was fabricated successfully with fully considering its binding to the primary sites in HSA. Molecular simulation was used to assist the probe design. Two ICT ligands DNPM and MPM were initially designed. Both DNPM and MPM had favorable HSA binding abilities, but only DNPM had a satisfactory HSA sensitivity. Electromagnetic coupling played a key role in DNPM fluorescence enhancement. Due to the electromagnetic environment difference in protein structure, DNPM only exhibited strong sensitivity to serum albumins. DNPM could bind to Sudlow site I and site II in HSA but could not be displaced from its binding sites by common site specific drugs (e.g. phenylbutazone and ibuprofen). Besides, DNPM exhibited great potential for illumining serum albumin in living cells. The results provided a beneficial approach for designing and synthesizing high sensitive and selective fluorescent probes for proteins.

Dietary polyphenols inhibit plasma protein arabinosylation: Biomolecular interaction of genistein and ellagic acid with serum albumins

The mode of interaction of polyphenolic compounds like genistein (GTN) and ellagic acid (EGA) with human and bovine serum albumin (HSA and BSA, respectively) was found to differ significantly. Stern-Volmer (SV) analysis of the fluorescence quenching data revealed that the binding strength of EGA (1.9 ± 0.09 × 105 M-1) to HSA is about one order of magnitude higher than GTN (2.24 ± 0.06 × 104 M-1). While the static quenching of HSA fluorescence was found to proceed through simple Stern-Volmer (SV) mechanism, a quenching sphere-of-action model was indispensable for BSA. Temperature dependent fluorescence along with a series of other biophysical experiments and ensemble docking calculation revealed that EGA and GTN bind to the serum proteins primarily through the entropy driven process. The α-helical content and the microenvironment near Trp residue of HSA and BSA did not show any appreciable change due to the binding of either GTN or EGA. Interestingly, both GTN and EGA were found to inhibit the formation of advanced glycated end (AGE) product of serum proteins up to the extent of 70-90% within 12-24 h. Relatively moderate binding propensity along with the anti-glycation ability of the polyphenols confirmed that GTN and EGA can be used either as an alternative or towards development of suitable drugs in the prevention of many diabetic-related complications.

How Different Albumin-Binders Drive Probe Distribution of Fluorescent RGD Mimetics

The biodistribution of medical imaging probes depends on the chemical nature of the probe and the preferred metabolization and excretion routes. Especially targeted probes, which have to reach a certain (sub)cellular destination, have to be guided to the tissue of interest. Therefore, small molecular probes need to exhibit a well-balanced polarity and lipophilicity to maintain an advantageous bioavailability. Labelled antibodies circulate for several days due to their size. To alter the biodistribution behavior of probes, different strategies have been pursued, including utilizing serum albumin as an inherent transport mechanism for small molecules. We describe here the modification of an existing fluorescent RGD mimetic probe targeted to integrin α_vβ₃ with three different albumin binding moieties (ABMs): a diphenylcyclohexyl (DPCH) group, a p-iodophenyl butyric acid (IPBA) and a fatty acid (FA) group with the purpose to identify an optimal ABM for molecular imaging applications. All three modifications result in transient albumin binding and a preservation of the target binding capability. Spectrophotometric measurements applying variable amounts of bovine serum albumin (BSA) reveal considerable differences between the compounds concerning their absorption and emission characteristics and hence their BSA binding mode. In vivo the modified probes were investigated in a murine U87MG glioblastoma xenograft model over the course of 1 wk by fluorescence reflectance imaging (FRI) and fluorescence mediated tomography (FMT). While the unmodified probe was excreted rapidly, the albumin-binding probes were accumulating in tumor tissue for at least 5 days. Considerable differences between the three probes in biodistribution and excretion characteristics were proved, with the DPCH-modified probe showing the highest overall signal intensities, while the FA-modified probe exhibits a low but more specific fluorescent signal. In conclusion, the modification of small molecular RGD mimetics with ABMs can precisely fine-tune probe distribution and offers potential for future clinical applications.

Polymethine Dyes as Probes for Detecting the SARS-COV-2 Coronavirus: In silico Molecular Docking Study

The noncovalent interaction between various polymethine dyes (45 compounds in total) and a spike protein (S), one of the main structural component of the SARS-CoV-2 coronavirus, is studied in silico (molecular docking) to develop effective probes to detect the virus. The interaction energies and the spatial configurations of the complexes of the dye molecules with S are found. We showed that cationic polymethine dyes and neutral squarylium dyes do not form stable complexes with S. Some anionic dyes having negative total energies E_tot may be recommended for practical research.

Stabilization of a potential anticancer thiosemicarbazone derivative in Sudlow site I of human serum albumin: In vitro spectroscopy coupled with molecular dynamics simulation

Human Serum Albumin (HSA) is the most important protein in human blood plasma and can acts as a major transporting agent for various drug molecules with flexible binding interaction. To elucidate the interaction of a newly designed potential anticancer thiosemicarbazone based luminophore (E)-1-(4-(diethylamino)-2-hydroxybenzylidene)-4,4-dimethyl-thiosemicarbazide (DAHTS) with HSA under physiological condition, in vitro optical spectroscopic experiments viz UV-Vis absorption, steady state fluorescence, fluroscence anisotropy, time resolved fluorscence (TRF) and cicular dichroism (CD) spectroscopy have been scrutinised. The experimental findings have been corroborated with in silico molecular docking analysis and Molecular Dynamics (MD) simulation. The spectroscopic results demonstrated that the conventionally anion-favouring Sudlow site I of HSA copiously adapt neutral DAHTS molecule with moderate binding affinity. The mean fluorescence lifetime of the sole tryptophan (Trp-214) present in the macromolecule experiences an appreciable diminution with an increase in concentration of the synthesized molecule. DAHTS localize itself close to Trp-214 within subdomain IIA (Sudlow site I) and surrounded by multiple hydrophobic amino acid residues (Val-235, Val-231, Ala-229, Phe-228, Val-325, Phe-326, Leu-327, Met-329, Phe-330, Leu-331, Tyr-332, Leu-346, Leu-347, Val-482, Leu-349, Ala-350, Ala-210, Trp-214, Ala- 213 and Val-216) in HSA. The distinct fluorescence lifetime, diverse pathways and changing rate of population indicates that the rotamerisation of Trp-214 residue is controlled by the guest molecule. Sudlow site I of HSA behaves flexibly and induces an allosteric modulation in the macromolecule resulting a minor deformation in the protein secondary structure as observed in CD (observed 11% change of α-helix content) as well as in MD simulation. The integrated multi-spectroscopic research described herein provides several important information about the binding interaction of a thiosemicarbazone Schiff base with HSA, which can be very significant for thiosemicarbazone based drug designing for academia as well as industry.