A Diversified Spectrometric and Molecular Docking Technique to Biophysical Study of Interaction between Bovine Serum Albumin and Sodium Salt of Risedronic Acid, a Bisphosphonate for Skeletal Disorders

Evaluation of the structure and stability of myoglobin after interaction with ribose: spectroscopic and molecular simulation approach

Osmolytes, as small organic molecules, possess a remarkable ability to exert protective effects on biomacromolecules, including proteins, while preserving their inherent functionality. Myoglobin, a globular protein comprising a sequence of 153 amino acids, fulfills a crucial biological role by exhibiting reversible oxygen binding capabilities and facilitating its efficient transfer to the muscular tissues. In this study, the effects of ribose on myoglobin protein in sodium phosphate buffer were studied by UV-Vis's spectrophotometry and spectrofluorimetric investigations at pH 7.4. Also, the interaction was theoretically studied through molecular dynamics simulation and molecular docking techniques. The results showed that the ribose stabilizes the protein structure by increasing the melting temperature (Tm) of myoglobin. The fluorescence intensity of myoglobin decreased with a static quenching mechanism at different temperatures. The thermodynamic data obtained from the experimental results also predicted that the intermolecular forces affecting the formation of a myoglobin-ribose complex are mainly the van der Waals interactions and hydrogen bindings. Theoretical molecular docking analyses unveiled the favored binding site of ribose within the structure of myoglobin. Subsequent molecular dynamics simulations validated the stability of the complex formed between ribose and myoglobin. Our findings are fundamental for understanding the molecular-level details of myoglobin-ligand interactions, opening avenues for innovative approaches to prevent or alleviate myoglobin dysfunction in various disease conditions.

Copper(II) and Zinc(II) Complexes with Bacterial Prodigiosin Are Targeting Site III of Bovine Serum Albumin and Acting as DNA Minor Groove Binders

The negative environmental and social impacts of food waste accumulation can be mitigated by utilizing bio-refineries' approach where food waste is revalorized into high-value products, such as prodigiosin (PG), using microbial bioprocesses. The diverse biological activities of PG position it as a promising compound, but its high production cost and promiscuous bioactivity hinder its wide application. Metal ions can modulate the electronic properties of organic molecules, leading to novel mechanisms of action and increased target potency, while metal complex formation can improve the stability, solubility and bioavailability of the parent compound. The objectives of this study were optimizing PG production through bacterial fermentation using food waste, allowing good quantities of the pure natural product for further synthesizing and evaluating copper(II) and zinc(II) complexes with it. Their antimicrobial and anticancer activities were assessed, and their binding affinity toward biologically important molecules, bovine serum albumin (BSA) and DNA was investigated by fluorescence emission spectroscopy and molecular docking. The yield of 83.1 mg/L of pure PG was obtained when processed meat waste at 18 g/L was utilized as the sole fermentation substrate. The obtained complexes CuPG and ZnPG showed high binding affinity towards target site III of BSA, and molecular docking simulations highlighted the affinity of the compounds for DNA minor grooves.

Exploring the interaction of a potent anti-cancer drug Selumetinib with bovine serum albumin: Spectral and computational attributes

The binding of drugs to plasma proteins determines its fate within the physiological system, hence profound understanding of its interaction within the bloodstream is important to understand its pharmacodynamics and pharmacokinetics and thereby its therapeutic potential. In this regard, our work delineates the mechanism of interaction of Selumetinib (SEL), a potent anti-cancer drug showing excellent effect against multiple solid tumors, with plasma protein bovine serum albumin (BSA), using methods such as absorption, steady-state fluorescence, time-resolved, fluorescence resonance energy transfer, Fourier transform infrared spectra (FTIR), circular dichroism (CD), synchronous and 3D-fluorescence, salt fluorescence, molecular docking and molecular dynamic simulations. The BSA fluorescence intensity was quenched with increasing concentration of SEL which indicates interactions of SEL with BSA. Stern-Volmer quenching analysis and lifetime studies indicate the involvement of dynamic quenching. However, some contributions from the static quenching mechanism could not be ruled out unambiguously. The association constant was found to be 5.34 × 105 M-1 and it has a single binding site. The Förster distance (r) indicated probable energy transmission between the BSA and SEL. The positive entropy changes and enthalpy change indicate that the main interacting forces are hydrophobic forces, also evidenced by the results of molecular modeling studies. Conformation change in protein framework was revealed from FTIR, synchronous and 3D fluorescence and CD studies. Competitive binding experiments as well as docking studies suggest that SEL attaches itself to site I (subdomain IIA) of BSA where warfarin binds. Molecular dynamic simulations indicate the stability of the SEL-BSA complex. The association energy between BSA and SEL is affected in the presence of different metals differently.

Interactions between polycyclic musks and human lactoferrin: Multi-spectroscopic methods and docking simulation

Galaxolide (1,3,4,6,7,8-hexahydro-4,6,6,7,8-hexamethylcyclopenta-γ-2-benzopyrane; HHCB) and Tonalide (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene; AHTN) are "pseudo-persistent" pollutants that can cause DNA damage, endocrine disruption, organ toxicity, and reproductive toxicity in humans. HHCB and AHTN are readily enriched in breast milk, so exposure of infants to HHCB and AHTN is of concern. Here, the molecular mechanisms through which HHCB and AHTN interact with human lactoferrin (HLF) are investigated using computational simulations and spectroscopic methods to identify indirectly how HHCB and AHTN may harm infants. Molecular docking and kinetic simulation studies indicated that HHCB and AHTN can interact with and alter the secondary HLF structure. The fluorescence quenching of HLF by HHCB, AHTN was static with the forming of HLF-HHCB, HLF-AHTN complex, and accompanied by non-radiative energy transfer and that 1:1 complexes form through interaction forces. Time-resolved fluorescence spectroscopy indicated that binding to small molecules does not markedly change the HLF fluorescence lifetime. Three-dimensional fluorescence spectroscopy indicated that HHCB and AHTN alter the peptide chain backbone structure of HLF. Ultraviolet-visible absorption spectroscopy, simultaneous fluorescence spectroscopy, Fourier-transform infrared spectroscopy, and circular dichroism spectroscopy indicated that HHCB and AHTN change the secondary HLF conformation. Antimicrobial activity experiments indicated that polycyclic musks decrease lactoferrin activity and interact with HLF. These results improve our understanding of the mechanisms involved in the toxicities of polycyclic musks bound to HLF at the molecular level and provide theoretical support for mother-and-child health risk assessments.

Investigation of the binding interactions between 17α-ethinylestradiol with bovine serum albumin by multispectroscopy

To understand the effect of 17α-ethinylestradiol (EE2) on the conformation changes of bovine serum albumin (BSA), the binding mechanisms of EE2 with BSA were investigated by fluorescence spectroscopy, time-resolved fluorescence spectroscopy, synchronous fluorescence spectroscopy, three-dimensional fluorescence spectroscopy, UV-visible spectroscopy, circular dichroism (CD) spectroscopy and molecular docking. The quenching constants, binding constants, the number of binding sites, thermodynamic parameters, binding distance and the secondary structure changes of BSA were determined. The results of fluorescence quenching experiment suggested that the fluorescence quenching of BSA by EE was due to the formation of complex through static quenching, which was also confirmed by time-resolved fluorescence measurements. The thermodynamic parameters indicated that the binding of EE2 to BSA was driven mainly by van der Waals forces and hydrogen bonding. The conformation alterations of BSA upon EE2 binding were studied by UV-vis spectroscopy and CD spectroscopy. The results of site marker competitive experiments and molecular docking showed that the binding sites of EE2 were mainly located within site I in the subdomain IIA of BSA.

Multispectral and computational probing of the interactions between sitagliptin and serum albumin

The binding of sitagliptin (SIT), an anti-diabetic drug, to human and bovine serum albumin (HSA and BSA; main serum transport proteins) was investigated using various spectroscopic and molecular docking techniques. The fluorescence data demonstrated that SIT quenched inherent fluorescence of these proteins through the formation of SIT-HSA/BSA complexes. The number of binding sites was obtained (~1) and binding constant (K_b) and effective quenching constant (K_a) were calculated as 10⁴ for both systems. Based on thermodynamic parameters, the van der Waals forces and hydrogen bonding were the most important forces in the interactions between HSA/BSA and SIT, and the complex formation processes were spontaneous. The results of UV-vis absorption and FT-IR spectroscopic revealed that SIT induces small conformational changes in the structure of the proteins (HSA/BSA). The synchronous fluorescence (SF) spectroscopy demonstrated that the binding of SIT with HSA/BSA had no effect on the polarity around Trp and Tyr residues. The CD spectra showed changes in the secondary and tertiary structures of both proteins with a decrease in α-helices contents and an increase in β-turn structures. The molecular docking and spectroscopic data verified the binding mechanisms between SIT and HSA/BSA, and revealed that SIT completely fits into the hydrophobic cavity between domain II and domain III of these proteins.