Exploring the binding of two potent anticancer drugs bosutinib and imatinib mesylate with bovine serum albumin: spectroscopic and molecular dynamic simulation studies

Comprehending the intermolecular interaction of dacomitinib with bovine serum albumin: experimental and theoretical approaches

Dacomitinib (DAC), as a member of tyrosine kinase inhibitors is primarily used to treat non-small cell lung cancer. The intermolecular interaction between DAC and bovine serum albumin (BSA) was comprehended with the help of experiments and theoretical simulations. The outcomes indicated that DAC quenched the endogenous fluorescence of BSA through static quenching mode. In the binding process, DAC was preferentially inserted into the hydrophobic cavity of BSA subdomain IA (site III), and a fluorescence-free DAC-BSA complex with molar ratio of 1:1 was generated. The outcomes confirmed that DAC had a stronger affinity on BSA and the non-radiative energy transfer occurred in the combination process of two. And, it can be inferred from the outcomes of thermodynamic parameters and competition experiments with 8-aniline-1-naphthalenesulfonic acid (ANS) and D-(+)- sucrose that hydrogen bonds (H-bonds), van der Waals forces (vdW) and hydrophobic forces had a significant impact in inserting DAC into the hydrophobic cavity of BSA. The outcomes from multi-spectroscopic measurements that DAC could affect the secondary structure of BSA, that was, α-helix content decreased slightly from 51.0% to 49.7%. Moreover, the combination of DAC and BSA led to a reduction in the hydrophobicity of the microenvironment around tyrosine (Tyr) residues in BSA while had little influence on the microenvironment of around tryptophan (Trp) residues. The outcomes from molecular docking and molecular dynamics (MD) simulation further demonstrated the insertion of DAC into site III of BSA and hydrogen energy and van der Waals energy were the dominant energy of DAC-BSA stability. In addition, the influence of metal ions (Fe3+, Cu2+, Co2+, etc.) on the affinity of the system was explored.Communicated by Ramaswamy H. Sarma.

Molecular interactions and binding dynamics of Alpelisib with serum albumins: insights from multi-spectroscopic techniques and molecular docking

Alpelisib (ALP) is a potent anti-cancer drug showing promising activity against advanced breast cancers. Hence, profound understanding of its binding dynamics within the physiological system is vital. Herein, we have investigated interaction of ALP with human serum albumin (HSA) and bovine serum albumin (BSA) using spectroscopic techniques like absorption, fluorescence, time-resolved, synchronous and 3D-fluorescence, FRET, FT-IR, CD, and molecular docking studies. The intrinsic fluorescence of both BSA and HSA quenched significantly by ALP with an appreciable red shift in its emission maxima. Stern-Volmer analysis showed increase in Ksv with temperature indicating involvement of dynamic quenching process. This was further validated by no significant change in absorption spectrum of BSA and HSA (at 280 nm) upon ALP interaction, and by results of fluorescence time-resolved lifetime studies. ALP exhibited moderately strong binding affinity with BSA (of the order 106 M-1) and HSA (of the order 105 M-1), and the major forces accountable for stabilizing the interactions are hydrophobic forces. Competitive drug binding experiments and molecular docking suggested that ALP binds to site I in subdomain IIA of BSA and HSA. The Förster distance r was found to be less than 8 nm and 0.5 Ro < r < 1.5 Ro which suggests possible energy transfer between donors BSA/HSA and acceptor ALP. Synchronous and 3D-fluoresecnce, FT-IR and CD studies indicated that ALP induces conformational changes of BSA and HSA upon interaction.Communicated by Ramaswamy H. Sarma.

Exploring the effect of surfactants on the interactions of manganese dioxide nanoparticles with biomolecules

Interactions of manganese dioxide nanoparticles (MnO2 NPs) with vital biomolecules namely deoxyribonucleic acid (DNA) and serum albumin (BSA) have been studied in association with different surfactants by using fluorescence (steady state, synchronous and 3D), UV-visible, resonance light scattering (RLS), dynamic light scattering (DLS), and sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The esterase activity of serum albumin was tested in associations with MnO2 NPs and surfactants. The antioxidant potential of prepared NPs was also evaluated (DPPH method). Gel electrophoresis was carried out to analyze the effect of MnO2 NPs and surfactants on DNA. Presence of CTAB, Tween 20, DTAB and Tween 80 enhanced nanoparticle-protein binding. Tween 20 based nanoparticle systems showed long-term stability and biocompatibility. The quenching of BSA fluorescence emission in presence of MnO2 NPs alone and along with Tween 20 revealed stronger association of nanoparticles with proteins. Enhancement in the esterase activity (BSA) was observed in the presence of Tween 20. Furthermore, radical scavenging activity showed highest antioxidant potential in presence of Tween 20. The enthalpy and entropy assessment for protein-NPs association showed the predominance of Vander Waals interactions and hydrogen bonding. The synchronous fluorescence analysis highlighted the involvement of tryptophan (Trp) in the MnO2 NPs-protein interactions. The study evaluates the influence of surfactant on the associations of MnO2 NPs with the essential biomolecules. The findings can be crucially utilized in designing biocompatible MnO2 formulations for long term applications.Communicated by Ramaswamy H. Sarma.

The small-molecule kinase inhibitor ceritinib, unlike imatinib, causes a significant disturbance of lipid membrane integrity: A combined experimental and MD study

Ceritinib and imatinib are small-molecule protein kinase inhibitors which are applied as therapeutic agents against various diseases. The fundamentals of their clinical use, i.e. their pharmacokinetics as well as the mechanisms of the inhibition of the respective kinases, are relatively well studied. However, the interaction of the drugs with membranes, which can be a possible cause of side effects, has hardly been investigated so far. Therefore, we have characterized the interaction of both drugs with lipid membranes consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) in the absence and in the presence of cholesterol. For determining the membrane impact of both drugs on a molecular level, different experimental (NMR, ESR, fluorescence) and theoretical (MD simulations) approaches were applied. The data show that ceritinib, in contrast to imatinib, interacts more effectively with membranes significantly affecting various physico-chemical membrane parameters like membrane order and transmembrane permeation of polar solutes. The pronounced membrane impact of ceritinib can be explained by a strong affinity of the drug towards POPC which competes with the POPC-cholesterol interaction by that attenuating the ordering effect of cholesterol. The data are relevant for understanding putative toxic and cytotoxic side effects of these drugs such as the triggering of cell lysis or apoptosis.

Exploring the binding characteristics of bovine serum albumin with tyrosine kinase inhibitor entrectinib: Multi-spectral analysis and theoretical calculation

Entrectinib (ENB) is one of multi-target tyrosine kinase inhibitors, which is mainly used for treating neurotrophic tyrosine receptor kinase gene fusion positive solid tumors. The binding characteristics of ENB and bovine serum albumin (BSA) were studied by experiments and theoretical calculations. The steady-state fluorescence showed that ENB quenched the fluorescence of BSA through mixed quenching, and ENB was dominated by static quenching at low concentration. ENB and BSA had a moderate affinity, formed a complex with a stoichiometric ratio of 1:1 and the binding constant of about 10⁵ M^-1 at 298 K, and Förster non-radiative energy transfer occurs. According to the driving force competition experiment, thermodynamic parameter analysis and theoretical calculation, hydrogen bond, van der Waals force and hydrophobic force were the main factors affecting the stability of the ENB-BSA complex. Molecular docking and site markers competition showed that ENB spontaneously bound to the Site III of BSA so that ENB could make the skeleton of BSA loose, the spatial structure of BSA changed (α-helix decreased by 3.1%, random coil increased by 1.7%), and the microenvironment of Tyr and Trp residues changed. The existence of Co²⁺ metal ions can enhance the binding effect, thus prolonging the half-life of ENB in vivo, which may improve the efficacy of ENB, while Ca²⁺, Cu²⁺ and Mg²⁺ metal ions will reduce the efficacy of ENB.

Analysis of the binding selectivity and inhibiting mechanism of chlorogenic acid isomers and their interaction with grass carp endogenous lipase using multi-spectroscopic, inhibition kinetics and modeling methods

Polyphenols are inhibitors for lipase, but the binding selectivity and mechanism of polyphenol isomers and how they interact with lipase are not clear. Here, chlorogenic acid (CGA) isomers, neochlorogenic acid (NCGA) and cryptochlorogenic acid (CCGA) were used to explore the binding selectivity and mechanism of lipase. An inhibition assay indicated that both CGA isomers had dose-dependent inhibitory effects on lipase; however, the inhibitory effect of NCGA was better (IC₅₀: 0.647 mg/mL) than that of CCGA (IC₅₀: 0.677 mg/mL). NCGA and CCGA formed complexes with lipase at a molar ratio of 1:1, and the electrostatic interaction force plays a major role in the lipase-CCGA system. Molecular dynamics studies demonstrated that NCGA had a greater impact on the structure of lipase. The multi-spectroscopic and modeling results explained the effects of micro-structural changes on the binding site, the interaction force and the inhibition rate of the isomers when they combined with lipase.

Investigating the Effect of Tyrosine Kinase Inhibitors on the Interaction between Human Serum Albumin by Atomic Force Microscopy

It is important for elucidating the regulation mechanism of life activities, as well as for the prevention, diagnosis, and drug design of diseases, to study protein–protein interactions (PPIs). Here, we investigated the interactions of human serum albumin (HSA) in the presence of tyrosine kinase inhibitors (TKIs: imatinib, nilotinib, dasatinib, bosutinib, and ponatinib) using atomic force microscopy (AFM). The distribution of rupture events including the specific interaction force F_i and the non-specific interaction force F₀ between HSA pairs was analyzed. Based on the force measurements, F_i and F₀ between HSA pairs in the control experiment were calculated to be 47 ± 1.5 and 116.1 ± 1.3 pN. However, F_i was significantly decreased in TKIs, while F₀ was slightly decreased. By measuring the rupture forces at various loading rates and according to the Bell equation, the kinetic parameters of the complexes were investigated in greater detail. Molecular docking was used as a complementary means by which to explore the force of this effect. The whole measurements indicated that TKIs influenced PPIs in a variety of ways, among which hydrogen bonding and hydrophobic interactions were the most important. In conclusion, these outcomes give us a better insight into the mechanisms of PPIs when there are exogenous compounds present as well as in different liquid environments.

Spectroscopic and in silico insight into the interaction between dicofol and human serum albumin

Dicofol, a broad-spectrum acaricide, has garnered considerable attention because of the potential harm to the environment and various organisms. Herein, this study applied spectroscopic and in silico methods to understand the interaction between human serum albumin (HSA) and dicofol. Fluorescence experiments demonstrated that dicofol formed a stable complex and the binding process occurred in Suldow's site I of HSA. Its binding constant was 2.26 × 10⁵ M^-1 at 298 K. Van der Waals forces and hydrogen bond were primarily facilitated the interaction between dicofol and HSA (ΔH < 0, ΔS < 0) according to thermodynamic experiments. Additionally, 3D fluorescence and circular dichroism (CD) spectra revealed a few conformational changes in HSA due to dicofol. Molecular docking analysis indicated that dicofol interacted with Ser192, Gln196, Leu481, Arg218, Leu238, and Phe211 via van der Waals forces and formed a hydrogen bond with His242. Molecular dynamics (MD) simulation showed that Lys195 and Arg218 residues contributed greater energy for forming the HSA-dicofol complex. MD simulation analysis also showed that dicofol can affect the HSA structure with a reduction in α-helix. This research is desired to facilitate a new perspective on the toxicity mechanism of dicofol in the human body.

Evaluation of the interaction of novel tyrosine kinase inhibitor apatinib mesylate with bovine serum albumin using spectroscopies and theoretical calculation approaches

Apatinib mesylate (APM), a novel tyrosine kinase inhibitor, has been applied in treating various cancers. In the present study, the binding mechanism of APM with bovine serum albumin (BSA) was studied by making use of various spectroscopic and theoretical calculation approaches to provide theoretical support for further studying its pharmacokinetics and metabolism. The results from fluorescence experiments showed that the quenching mechanism of BSA induced by APM was static quenching and the APM-BSA complex with the stoichiometry of 1:1 was formed during binding reaction. Moreover, the findings also showed that the binding process of APM to BSA was spontaneous and enthalpy-driven, and the mainly driving forces were hydrogen bonding, van der Waals as well as hydrophobic interactions. From the outcomes of the competitive experiments, it can be found that the binding site was primarily nestled in sub-domain IIIA of BSA (site II) which was in line with the results of molecular docking. An appreciable decline in α-helix content of BSA can be observed from the FT-IR data, meaning that the conformational change of BSA occurred after binding with APM, this phenomenon can be corroborated by the results of UV-vis, synchronous fluorescence and 3D fluorescence studies. Furthermore, the effect of some metal ions (e.g. K⁺, Co²⁺, Ni²⁺, Fe³⁺) on the binding constant of APM to BSA was explored.Communicated by Ramaswamy H. Sarma.

Investigation of the binding interactions between dimethyl phthalate and its metabolite with bovine serum albumin by multispectroscopy

To understand the behavior of dimethyl phthalate (DMP) and realize the effect of DMP and its metabolite, monomethyl phthalate (MMP), on the conformation changes of bovine serum albumin (BSA), the interaction mechanisms of DMP and MMP with BSA were investigated by multispectroscopy and molecular docking. The results of the fluorescence quenching experiment showed that the fluorescence quenching of BSA by DMP and MMP was due to the formation of a complex though static quenching, which was also confirmed by time-resolved fluorescence measurements. The binding constants were 8.06 × 10⁴ M^-1 and 4.74 × 10⁴ M^-1 for DMP-BSA and MMP-BSA, respectively, and the number of binding sites were 1.20 (DMP) and 1.18 (MMP). The thermodynamic parameters showed different binding forces for DMP and MMP with BSA. The binding of DMP to BSA was driven mainly by hydrophobic interactions and hydrogen bonding, and MMP bound to BSA by van der Waals forces and hydrogen bonding, which were in accordance with the results from the molecular docking. The conformation and structural alterations of BSA upon DMP or MMP binding were studied by UV-vis spectroscopy, circular dichroism spectroscopy and synchronous fluorescence spectroscopy. The presence of metabolite did not change the quenching mechanism but decreased the binding affinity of DMP toward BSA as well as shortened the binding distance, which may be attributed to the competition between DMP and MMP for binding to BSA. This study revealed the combined effects of DMP and its metabolite on BSA at the molecular level.

Investigation on the interaction between triclosan and bovine serum albumin by spectroscopic methods

Multi-spectroscopic and molecular docking methods were used to study the interaction between triclosan (TCS) and bovine serum albumin (BSA). The results indicated that the fluorescence quenching of BSA by TCS was due to the formation of TCS-BSA complex through static quenching. This result was also demonstrated by time-resolved fluorescence experiment. The binding constants and number of binding sites between TCS and BSA were 1.30 × 10⁵ M^-1 and 1.17 at 298 K, respectively. The thermodynamic parameters were studied in detail which suggested that hydrophobic forces and hydrogen bond played major roles in the TCS-BSA interaction. Moreover, the site marker competitive experiments and docking studies revealed that TCS could bind BSA into site I in subdomain IIA. All the results of UV-vis spectrophotometry, circular dichroism spectroscopy and synchronous fluorescence spectroscopy showed that interaction between TCS and BSA induced conformation changes of BSA.

Interaction mechanism of olaparib binding to human serum albumin investigated with NMR relaxation data and computational methods

The interaction mechanism between olaparib (OLA) and human serum albumin (HSA) has been investigated using experimental and computational techniques. An NMR relaxation approach based on the analysis of proton selective and non-selective spin-lattice relaxation rates at different temperatures can provide quantitative information about the affinity index and the thermodynamic equilibrium constant of the OLA-HSA system. The affinity index and the thermodynamic equilibrium constant decreased as temperature increased, indicating that the interactions between OLA and HSA could be weakened as temperature increased. Molecular docking and dynamics simulations revealed that OLA stably bound to subdomain II (site 1), and OLA could induce the conformational and micro-environmental changes in HSA. CD results suggested that α-helix content decreased after OLA was added, demonstrating that OLA affected the secondary structure of HSA.