Interaction of novel benzanthrone derivative with amyloid lysozyme

A novel benzanthrone derivative AM18 was investigated with respect to its photophysical properties when bound to native, oligomeric and fibrillar hen egg white lysozyme. As shown by fluorimetric titration AM18 is more sensitive to pathogenic protein aggregates than Thioflavin T, however has no ability to differentiate between mature and immature lysozyme fibrils. The recovered affinity and fluorescence response of the novel probe to amyloid protein appeared to be similar to those of recently developed amyloid lysozyme-sensitive dyes like e. g. Nile Red and cyanine dye 7515. Despite the high increase of the probe emission in the presence of amyloid lysozyme compared to its fluorescence in buffer, the minimal amount that could be detected by 1 μM AM18 was 10 times lower for amyloid-native protein solutions due to high affinity of the dye for lysozyme monomers. In general, because of high quantum yields and “signal-to-noise” ratios in the presence of pathogenic protein aggregates AM18 appeared to be an effective tool for amyloid detection and characterization in vitro, being however unable to detect pathogenic protein aggregates in vivo like e.g. recently reported p-FTAA because of the sensitivity to lipids. Compared to previously reported AM3 a novel dye showed 2-fold lower “signal-to- noise” ratio in the presence of fibrillar lysozyme, and 2 fold lower blue shift of emission maximum. This tendency was explained in terms of decreased charge transfer from the donor to acceptor groupes of AM18 compared to AM3. Finally, as concluded from the comparison of AM18 and previously studied benzanthrone derivatives, the 5 nm – red edge excitation shift of AM18 is indicative of its possible binding to fibril “deep cavities”, containing no water. High anisotropy values of amyloid-bound dye led us to conclusion that the enhanced fluorescence of the probe is associated with the decrease of the rotational motion of the amino-substitute about the benzanthrone unit. This is a sign of AM18 behaviour as a molecular rotor

Spectral behavior of novel benzanthrone probe in model membranes

The present study was undertaken to evaluate the sensitivity of a newly synthesized benzanthrone dye to the changes in physicochemical properties of lipid bilayer. It was shown that the dye under study is non- emissive in buffer but exhibites strong fluorescence in lipid phase. Partitioning of AM15 into model membranes composed of zwitterionic lipid phosphatidylcholine (PC) and its mixtures with anionic lipid cardiolipin and cholesterol was followed by significant increase of fluorescence quantum yield. Analysis of the partition coefficients showed that inclusion of cardiolipin and choleterol into phosphatidylcholine bilayer gives rise to the decrease of AM15 incorporation into lipid phase compared to the neat phosphatidylcholine membrane. It is assumed that AM15 resides in the hydrophobic bilater region, being oriented parallel to the lipid acyl chains

Molecular Docking Study of the Interactions Between Cyanine Dyes And DNA

Among the various fluorescent probes currently used for biomedical and biochemical studies, significant attention attracts cyanine dyes possessing advantageous properties upon their complexation with biomolecules, particularly nucleic acids. Given the wide range of cyanine applications in DNA studies, a better understanding of their binding mode and intermolecular interactions governing dye-DNA complexation would facilitate the synthesis of new molecular probes of the cyanine family with optimized properties and would be led to the development of new cyanine-based strategies for nucleic acid detection and characterization. In the present study molecular docking techniques have been employed to evaluate the mode of interaction between one representative of monomethines (AK12-17), three trimethines (AK3-1, AK3-3, AK3-5), three pentamethines (AK5-1, AK5-3, AK5-9) and one heptamethine (AK7-6) cyanine dyes and B–DNA dodecamer d(CGCGAATTCGCG)2 (PDB ID: 1BNA). The molecular docking studies indicate that: i) all cyanines under study (excepting AK5-9 and AK7-6) form the most stable dye-DNA complexes with the minor groove of double-stranded DNA; ii) cyanines AK5-9 and AK7-6 interact with the major groove of the DNA on the basis of their more extended structure and higher lipophilicity in comparison with other dyes; iii) cyanine dye binding is governed by the hydrophobic and Van der Waals interactions presumably with the nucleotide residues C9A, G10A (excepts AK3-1, AK3-5), A17B (excepts AK3-5, AK5-3) and A18B in the minor groove and the major groove residues С16B, A17B, A18B, C3A, G4A, A5A, A6A (AK5-9 and AK7-6); iv) all dyes under study (except AK3-1, AK3-5 and AK5-39 possess an affinity to adenine and cytosine residues, whereas AK3-1, AK3-5 and AK5-3 also interact with thymine residues of the double-stranded DNA

Association of novel monomethine cyanine dyes with bacteriophage MS2:A fluorescence study

Novel monomethine cyanine dyes Cl-YO, F-YO, Cl-YO-Et, Cl-YO-Bu, and YO-Pent were evaluated as agents to detect and characterise a small virus, the MS2 bacteriophage, using the dye and virus intrinsic fluorescence, kinetic and thermal properties, chemical denaturation, and molecular docking and quantum chemistry modelling. The examined compounds demonstrated enhanced fluorescence responses and high affinities (~1 μM−1) for the intact bacteriophage at physiological ionic strength. The linear Scatchard plots revealed the existence of one binding mode for most dyes. Strong evidence that the cyanines bind to the bacteriophage external surface were obtained, although the possibility of the dye penetration through the virus shell and subsequent complexation with the viral RNA was also tested. The main arguments in favour of the former were that i) the fluorescence of the MS2-bound fluorophores decreased under the influence of protein denaturants, urea and guanidine hydrochloride; ii) the fluorescence responses of the dyes to MS2 and bovine serum albumin were similar; and (iii) one order of magnitude higher sensitivity of the dyes to the yeast RNA was found. Simple docking studies suggested that one cyanine molecule is trapped in a cleft formed by three proteins composing the virus shell. Significant role of electrostatic forces in the stabilisation of the dye-MS2 complexes at low ionic strength (10 mM) was demonstrated, while the influence of steric, hydrophobic, and van-der-Waals interactions was expected to increase at physiological ionic strength. The spectral properties of the novel cyanine dyes compared to other fluorophores demonstrated higher sensitivity of the cyanines to MS2, rendering them promising agents for the investigation of the changes in the virus structure under the influence of heat (Cl-YO-Et, Cl-YO-Bu), denaturants (Cl-YO, F-YO), and ionic strength (all the compounds)

Molecular Dynamics Study of The Lysozyme-Based Drug Delivery Nanosystems Loaded with Antiviral Drugs and Cyanine Dyes

Protein-based drug nanocarriers are increasingly recognized as promising candidates for effective drug delivery, owing to a multitude of beneficial advantages over synthetic materials including low cytotoxicity, biocompatibility, biodegradability, abundance, renewability, and high drug loading capacity mediated by diverse functional groups and interactions. In the present study the molecular dynamics simulation was employed to explore the stability of lysozyme-based drug delivery nanosystems functionalized by the antiviral drugs (favipiravir, molnupiravir, nirmatrelvir and ritonavir) and cyanine dyes (AK7-5, AK5-6, AK3-11). A series of 5 ns or 100 ns MD simulations for the top-scored docked drug-dye-protein complexes, obtained using the PatchDock server was performed at 310 K with GROMACS software using the CHARMM General Force Field. The MD results have been analyzed in terms of the parameters, such as the backbone root mean-square deviation, gyration radius, solvent accessible surface area, the root means square fluctuations. The analysis of calculated parameters for the studied systems enabled us to improve the previously acquired molecular docking data. Taken together, the results obtained indicate that Lz-F-AK3-11, Lz-R-AK75, Lz-R-AK56, Lz-N-AK75, Lz-N-AK3-11, and Lz-M-AK75 systems exhibit the highest stability among the examined dye-drug-protein systems and represent potential candidates for the targeted delivery of the explored antiviral agents

Spectral behavior of novel benzanthrone probe in model membranes

The present study was undertaken to evaluate the sensitivity of a newly synthesized benzanthrone dye to the changes in physicochemical properties of lipid bilayer. It was shown that the dye under study is non- emissive in buffer but exhibites strong fluorescence in lipid phase. Partitioning of AM15 into model membranes composed of zwitterionic lipid phosphatidylcholine (PC) and its mixtures with anionic lipid cardiolipin and cholesterol was followed by significant increase of fluorescence quantum yield. Analysis of the partition coefficients showed that inclusion of cardiolipin and choleterol into phosphatidylcholine bilayer gives rise to the decrease of AM15 incorporation into lipid phase compared to the neat phosphatidylcholine membrane. It is assumed that AM15 resides in the hydrophobic bilater region, being oriented parallel to the lipid acyl chains