Exploring the impact of novel thiazole-pyrazole fused benzo-coumarin derivatives on human serum albumin: Synthesis, photophysical properties, anti-cholinergic activity, and interaction studies

Derivatives of thiazole-pyrazole fused benzo-coumarin compounds were successfully synthesized and characterized, followed by a comprehensive spectroscopic investigation on various photophysical properties in different media. The multipronged approach using steady state and time resolved fluorescence spectroscopy pointed out the impact of substitution in the estimated spectroscopic and other physicochemical properties of the systems. Further, the evaluation of anti-acetylcholinesterase (anti-AChE) activity yielded significant insight into the therapeutic potential of the synthesized coumarinyl compounds for the treatment of Alzheimer's disease (AD). The findings revealed a non-competitive mode of inhibition mechanism, with an estimated IC50 value of 67.72 ± 2.00 nM observed for one of the investigated systems as AChE inhibitor. Notably, this value is even lower than that of an FDA-approved AD drug Donepezil (DON), indicating the enhanced potency of the coumarin derivatives in inhibiting AChE. Interestingly, significant diminution in inhibition was observed in presence of human serum albumin (HSA) as evidenced by the relative increase in IC50 value by 8 ∼ 39 % in different cases, which emphasized the role of albumin proteins to control therapeutic efficacies of potential medications. In-depth spectroscopic and in-silico analysis quantified the nature of interactions of the investigated systems with HSA and AChE. Overall, the outcomes of this study provide significant understanding into the biophysical characteristics of novel thiazole-pyrazole fused benzo-coumarin systems, which could aid in the development of new cholinergic agents for the treatment of AD and materials based on coumarin motifs.

A chromatographic method for determining the interaction between a drug and two target proteins by fabricating a dual-heterogeneous surface

Characterization of the drug-target interactions is pivotal throughout the whole procedure of drug development. Most of the current assays, particularly, chromatographic methods lack the capacity to reveal drug adsorption on the muti-target surface. To this end, we derived a reliable and workable mathematical equation for revealing drug bindings to dual targets on the heterogeneous surface starting from the mass balance equation. The derivatization relied on the correlation of drug injection amounts with their retention factors. Experimental validation was performed by determining the binding parameters of three canonical drugs on a heterogeneous surface, which was fabricated by fusing angiotensin receptor type I and type II receptors (AT1R and AT2R) at the terminuses of circularly permuted HaloTag (cpHaloTag) and immobilizing the whole fusion protein onto 6-bromohexanoic acid modified silica gel. We proved that immobilized AT1R-cpHalo-AT2R maintained the original ligand- and antibody-binding activities of the two receptors in three weeks. The association constants of valsartan, candesartan, and telmisartan to AT1R were (6.26±0.14) × 105, (9.66±0.71) × 105, and (3.17±0.03) × 105 L/mol. In the same column, their association constants to AT2R were (1.25±0.04) × 104, (2.30±0.08) × 104, and (8.51±0.06) × 103 L/mol. The patterns of the association constants to AT1R/AT2R (candesartan>valsartan>telmisartan) were in good line with the data by performing nonlinear chromatography on control columns containing immobilized AT1R or AT2R alone. This provided proof of the fact that the derivatization allowed the determination of drug bindings on the heterogeneous surface with the utilization of a single series of injections and linear regression. We reasoned that is simple enough to model the bindings of drug adsorption on commercially available adsorbents in fundamental or industrial fields, thus having the potential to become a universal method for analyzing the bindings of a drug to the heterogeneous surface containing multiple targets.

Probing the interaction of cephalosporin antibiotic "cefoperazone" with lysozyme using spectroscopic and in silico methods: Effect of paracetamol on binding

The interaction of lysozyme with cefoperazone was studied by means of spectroscopic and computational approaches. The change in the UV-visible spectrum of lysozyme in presence of cefoperazone was an indication of the complex formation between them. Fluorescence spectroscopy suggested that there was a fair interaction between the protein and drug which was taken place via dynamic quenching mechanism and the binding ratio was approximately 1:1. The binding was energetically feasible and principally supported by the hydrophobic forces. CD spectroscopic studies have shown that cefoperazone induced the secondary structure of lysozyme by increasing the α-helical contents of the latter. In silico studies revealed that the large nonpolar cavity was the preferred binding site of cefoperazone within lysozyme and the interaction was taken place mainly through hydrophobic forces with small involvement of hydrogen bonding and electrostatic interactions which is in good agreement with the experimental analyses. Effect of paracetamol was also seen on the binding and it was found that paracetamol had a negative influence on the binding between cefoperazone and lysozyme.

Mahalanobis distance correlation: A novel approach for quantitating changes in multidimensional NMR spectra in biological applications

We present here a novel protocol for quantitating changes in the NMR spectra, which is based on Mahalanobis statistics. In a two dimensional NMR spectrum, the various peaks are taken to represent a distribution, and the two chemical shifts along the orthogonal axes and the peak intensities constitute three observables. All these observables vary in a correlated manner. Taking account of these, the Mahalanobis distance (MD) reflects the distance of any chosen peak from the centre of the distribution. For quantitating changes in a particular spectrum (say A) with N peaks (altered protein NMR spectrum) with respect to a reference spectrum (say B) with M peaks (original protein NMR spectrum), a composite spectrum with N + M peaks is generated. A one-to-one correspondence between N MD values considering all the N peaks in A and the same N peaks in the composite spectrum (A + B) is calculated. The MD distance of corresponding peaks in two different distributions can be correlated to assess the changes in the spectra during the course of a biological phenomenon, or as a result of biomolecular interactions. We have demonstrated these ideas, first, using the ¹H-¹⁵N HSQC spectrum of Ubiquitin, and then application of these has been demonstrated for monitoring progression of fibrillation of the protein α-Synuclein, in absence and presence of safranal, a known inhibitor of fibrillation of the protein. The method is in general applicable to multidimensional NMR spectra, does not require extensive data collection, and allows quantitative assessment of spectral changes via a single parameter. We believe that the method will have wide ranging applications to monitor many biological phenomena, and will also be useful in an industrial environment for mass comparison of molecules in a rapid manner.

Immobilization of peroxisome proliferator-activated receptor gamma and the application in screening modulators of the receptor from herbal medicine

Screening and identification of potential compounds from herbal medicine is a prevailing way to find a lead for the development of innovative drugs. This promotes the development of new methods that are feasible in complex matrices. Here, we described a one-step reversible methodology to immobilize nuclear peroxisome proliferator-activated receptor gamma (PPARγ) onto amino microsphere coated with a DNA strand specifically binding to the receptor. The specific interaction allowed us to achieve the immobilization of PPARγ by mixing the DNA modified microspheres with E. coli lysates expressing the receptor. Characterization of the immobilized receptor was carried out by morphology and binding specificity analysis. Feasibility of immobilized PPARγ in the drug-receptor interaction analysis was performed by an injection amount-dependent method. Besides, immobilized PPARγ was also applied in screening modulators of the receptor from Coptidis Rhizoma extract. The binding of the screened compounds to PPARγ was examined by time-resolved fluorescence resonance energy transfer assay. The results showed that immobilized PPARγ was stable for thirty days with a high-specificity of ligand recognition at the subtype receptor level. Berberine and palmatine were the bioactive compounds of Coptidis Rhizoma specifically binding to PPARγ. The two compounds exhibited half maximal inhibitory concentrations of 4.11 and 2.98 μM during their binding to the receptor. We concluded that the current method is possible to become a common strategy for the immobilization of nuclear receptors, and the immobilized receptor is a high throughput method for recognizing and separating the receptor modulators from complex matrices including herbal medicine.

Fluorescence Enhancement Based Quantification of Human Serum Albumin from Biological Sample Using Indole Based Nanosuspension: Molecular Interactions and Molecular Docking Studies

Fluorescent 3-[(E)-(2-phenylhydrazinylidene) methyl]-1H-indole (PHI) was synthesized by condensation of indole-3-carboxaldehyde and phenyl hydrazine in presence of acetic acid and ethanol and after spectral characterization used further to prepare its aqueous nano suspension by reprecipitation method using polyvinylpyrrolidone (PVP) as stabilizer. The average particle size of nano suspension measured by Dynamic Light Scattering (DLS) was found 77.5 nm while FESEM microphotograph showed spherical morphology. The blue shift in the absorption spectrum and stokes shifted fluorescence of nanosuspension of PHI compared to its monomer spectrum in dilute solution indicate formation of H-type aggregate by face to face overlapping of the molecules.The aggregation induced enhanced emission (AIEE) of PVP capped nanosuspension of PHI is increased appreciably by presence of aqueous solution of human serum albumin (HSA). A suitable mechanism of molecular binding interactions based on complex formation between PHI nanoaggregate and HSA through PVP is proposed. Fluorescence life time, zeta potential and particle size data of PHI nanoparticles (PHINPs) obtained in presence of different amounts of HSA are in support of molecular interactions leading to complex formation. The molecular docking studies showed that HSA and PVP capped PHINPs exhibit strong hydrogen bonding interaction. The fluorescence enhancement effect induced in PHI nanosuspension is used further to develop analytical method for quantitative estimation of HSA in aqueous biological sample solution.

Stable SERS substrate based on highly reflective metal liquid-like films wrapped hydrogels for direct determination of small molecules in a high protein matrix

The study of the interaction between small molecules and proteins is important. Surface-enhanced Raman spectroscopy (SERS) is suitable for such applications since it has the power of detecting a molecule based on its intrinsic nature and without labeling. Herein, the MeLLFs@PAAG SERS substrate supporting highly reflective metal liquid-like films (MeLLFs) with polyacrylamide hydrogels (PAAG) has high-density "hot spots" to provide excellent SERS activity. The MeLLFs@PAAG formed by AgNPs only has less than 15% SERS activity loss when stored in the air for more than three weeks. By using rhodamine 6G (R6G) as a model analyte, the AgNPs based MeLLFs@PAAG SERS substrate exhibits an enhancement factor (EF) as high as 8.0 × 10⁶, a limit of detection (LOD) of 76.8 pM (S/N = 3). Also, the formed PAAG provided a 3D molecular network to orderly secure the assembled nanoparticles (NPs), which not only improves the stability of NPs but also shields the Raman signal of proteins as high as 45 g/L allowing the direct determination of the binding rate of human serum albumin (HSA) and doxorubicin (DOX). A binding rate of about 70% was detected, which is consistent with previous reports. Thus, proposed the MeLLFs@PAAG SERS substrate can be used as a promising candidate for SERS measurement in complex biological samples.

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.

Halo-tagged protein immobilization: Effect of halide linkers on peak profile and drug-protein interaction

In previous work, we have established a one-step method to immobilize halo-tagged proteins onto microspheres through the covalent bond formed between the halo-tag and the halide linkers on the support surface. We observe extremely tailed peaks of most of drugs on the immobilized proteins, which is reasoned by the nonspecific interaction between the linkers and the drugs. To prove this, the current work designed five different halide linkers for the immobilization of beta₂-adrenoceptor (β₂-AR). We applied the immobilized receptor to systematically realize the effects of these halide linkers on drug-receptor interaction by analyzing peak profiles of five drugs. The retention times and the half-widths of the drugs appeared to be negatively correlated to the atom numbers of the linkers in the range of 6-13 atoms. Subsequent increase of linker atoms resulted in reduced retention times and wider peaks of the drugs. Applying identical linker length, we observed clear reduced retention times and half-widths of the five drugs than the linker in the absence of oxygen atom. Such improvement was dominated by the number of oxygen atoms. These indicated that linker S-4 (2-(2-(2-(2-chloroethoxy) ethoxy) ethoxy) acetic acid) was optimal to eliminate the unwanted non-specific interactions. In comparison with the columns prepared by linker S-1 (6-chlorocaproic acid) and histidine tagged β₂-AR, the drugs on the linker S-4 column gave greater dissociation rate constants (e.g. 60.3±0.3 s^-1 for salbutamol), which is closer to the data in literatures. Taking together, we concluded that optimization of the linker structure plays particular role in reducing the non-specific interaction between the immobilized protein and the drugs, thereby making the determination of drug-protein interaction more reliable.

The reorganization of conformations, stability and aggregation of serum albumin isomers through the interaction of glycopeptide antibiotic teicoplanin: A thermodynamic and spectroscopy study

The drugs-protein binding study is of growing importance for drug-repurposing against amyloidosis. In this work, we study the binding of teicoplanin (TPN), a glycopeptide antibiotic, with bovine serum albumin (BSA) in its neutral (N), physiological (P) and basic (B) forms, which exist at pH 6, pH 7.4 and pH 9, respectively. The binding and thermodynamic parameters of TPN binding were determined by isothermal titration calorimetry (ITC) and fluorescence quench titration methods. Two binding sites were observed for N and P forms, whereas B form showed only one binding site. ITC and molecular docking results indicated that TPN-BSA complex formation is stabilized by hydrogen bonds, salt bridges and hydrophobic interaction. The red-edge excitation shift (REES) study indicated an ordered compact and spatial arrangement of the TPN bound protein molecule. TPN was found to affect the secondary and tertiary structures of B form only. The TPN binding was observed to marginally stabilize BSA isomers. TPN was also found to inhibit BSA aggregation as monitored by Rayleigh light scattering and thioflavin T binding assay. The current in vitro study will open a new path to explore the possible use of TPN as potential drugs to treat amyloidosis.

Reversible and site-specific immobilization of β2-adrenergic receptor by aptamer-directed method for receptor-drug interaction analysis

Immobilized protein makes a profound impact on the development of assays for drug discovery, diagnosis and in vivo biological interaction analysis. Traditional methods are enormously challenged by the G-protein coupled receptor ascribed to the loss of receptor functions. We introduced a β₂-adrenergic receptor (β₂-AR) aptamer into the immobilization of the receptor. This was achieved by mixing the receptor conjugated silica gel with cell lysates containing the receptor. We found that the aptamer-directed method makes immobilized β₂-AR good stability in seven days and high specificity of ligand recognition at the subtype receptor level. Feasibility of the immobilized β₂-AR in drug-receptor interaction analysis was evaluated by injection amount-dependent method, nonlinear chromatography, and peak decay analysis. Salbutamol, methoxyphenamine, ephedrine hydrochloride, clorprenaline, tulobuterol, bambuterol, propranolol and ICI 118551 bound to the receptor through one type of binding sites. The association constants presented good agreement within the three methods but exhibited clear differences from the data by radio-ligand binding assay. Regarding these results, we concluded that the aptamer-directed method will probably become an alternative for reversible and site-specific immobilization of GPCRs directly from complex matrices; the immobilized receptor is qualitative for drug-receptor interaction analysis.

Immobilized angiotensin II type I receptor: A powerful method of high throughput screening for antihypertensive compound identification through binding interaction analysis

The enormous growth in drug discovery paradigm has necessitated continuous exploration of new methods for drug-protein interaction analysis. To enhance the role of these methodologies in designing rational drugs, this work extended an immobilized angiotensin II type I receptor (AT1R) based affinity chromatography in antihypertensive compound identification. We fused haloalkane dehalogenase at C-terminus of AT1R and expressed the fusion receptor in E. coli. The expressed receptor was covalently immobilized onto 8.0 μm microspheres by mixing the cell lysate with 6-chlorocaproic acid-modified amino polystyrene microspheres. The immobilized AT1R was utilized for thermodynamic and kinetic interaction analysis between the receptor and four specific ligands. Following confirmation of these interactions by molecular docking, we identified puerarin and rosmarinic acid by determining their binding to the receptor. Azilsartan, candesartan, valsartan and olmesartan displayed two kinds of binding sites to AT1R by injection amount-dependent method. By molecular docking, we recognize the driving forces of the interaction as electrostatic interaction, hydrogen bonds and van der Waals force. The dissociation rate constants (kd) of azilsartan, candesartan, valsartan and olmesartan to AT1R were 0.01138 ± 0.003, 0.05142 ± 0.003, 0.07547 ± 0.004 and 0.01310 ± 0.005 min-1 by peak profiling assay. Comparing with these parameters, puerarin and rosmarinic acid presented lower affinity (KA: 0.12 × 104 and 1.5 × 104/M) and slower kinetics (kd: 0.6864 ± 0.03 and 0.3005 ± 0.01 min-1) to the receptor. These results, taking together, indicated that the immobilized AT1R has the capacity to probe antihypertensive compounds.

Exploration of interaction scoring criteria in the CANDO platform

OBJECTIVE

Ascertain the optimal interaction scoring criteria for the Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun drug repurposing to improve benchmarking performance, thereby enabling more accurate prediction of novel therapeutic drug-indication pairs.

RESULTS

We have investigated and enhanced the interaction scoring criteria in the bioinformatic docking protocol in the newest version of our platform (v1.5), with the best performing interaction scoring criterion yielding increased benchmarking accuracies from 11.7% in v1 to 12.8% in v1.5 at the top10 cutoff (the most stringent one) and correspondingly from 24.9 to 31.2% at the top100 cutoff.

Molecular interaction study of an anticancer drug, ponatinib with human serum albumin using spectroscopic and molecular docking methods

Binding of a potent anticancer agent, ponatinib (PTB) to human serum albumin (HSA), main ligand transporter in blood plasma was analyzed with several spectral techniques such as fluorescence, absorption and circular dichroism along with molecular docking studies. Decrease in the K_SV value with increasing temperature pointed towards PTB-induced quenching as the static quenching, thus affirming complexation between PTB and HSA. An intermediate binding affinity was found to stabilize the PTB-HSA complex, as suggested by the K_a value. Thermodynamic analysis of the binding phenomenon revealed participation of hydrophobic and van der Waals interactions along with hydrogen bonds, which was also supported by molecular docking analysis. Changes in both secondary and tertiary structures as well as in the microenvironment around Trp and Tyr residues of HSA were anticipated upon PTB binding to the protein, as manifested from circular dichroism and three-dimensional fluorescence spectra, respectively. Binding of PTB to HSA led to protein's thermal stabilization. Competitive ligand displacement experiments using different site markers such as warfarin, indomethacin and ketoprofen disclosed the binding site of PTB as Sudlow's site I in HSA, which was further confirmed by molecular docking analysis.

Biomolecular interactions of amphotericin B nanomicelles with serum albumins: A combined biophysical and molecular docking approach

In this work, we investigated the interaction of amphotericin B (AmB) nanomicelles on the binding affinity and conformational change of human serum albumin (HSA) in comparison with bovine serum albumin (BSA) under physiological conditions by conducting several spectroscopic techniques further confirmed through molecular docking approaches. The experimental results showed that AmB nanomicelles could bind to both HSA and BSA to form protein/drug complexes with one binding site, and the binding process was spontaneous under physiological conditions. Fluorescence studies revealed that the quenching mechanism of these complexes was static quenching rather than dynamic quenching and exhibited strong binding between serum albumin and AmB nanomicelles. The results from UV-Visible spectra, FT-IR spectra, and CD spectra revealed that the AmB formulations affected the structure of both HSA and BSA proteins by changing the microenvironment around the tryptophan residues of protein and caused a secondary structure change of the protein with the loss of helical stability. The molecular docking experiments also supported the above results and effectively proved the binding and changes in the conformation of serum albumins by AmB micelles. This finding provides information of in vitro drug-plasma protein interactions for further study on the AmB binding mechanism and the pharmacodynamics and pharmacokinetics.

Binding of an anticancer drug, axitinib to human serum albumin: Fluorescence quenching and molecular docking study

Binding characteristics of a promising anticancer drug, axitinib (AXT) to human serum albumin (HSA), the major transport protein in human blood circulation, were studied using fluorescence, UV-vis absorption and circular dichroism (CD) spectroscopy as well as molecular docking analysis. A gradual decrease in the Stern-Volmer quenching constant with increasing temperature revealed the static mode of the protein fluorescence quenching upon AXT addition, thus confirmed AXT-HSA complex formation. This was also confirmed from alteration in the UV-vis spectrum of HSA upon AXT addition. Fluorescence quenching titration results demonstrated moderately strong binding affinity between AXT and HSA based on the binding constant value (1.08±0.06×10(5)M(-1)), obtained in 10mM sodium phosphate buffer, pH7.4 at 25°C. The sign and magnitude of the enthalpy change (∆H=-8.38kJmol(-1)) as well as the entropy change (∆S=+68.21Jmol(-1)K(-1)) clearly suggested involvement of both hydrophobic interactions and hydrogen bonding in AXT-HSA complex formation. These results were well supported by molecular docking results. Three-dimensional fluorescence spectral results indicated significant microenvironmental changes around Trp and Tyr residues of HSA upon complexation with AXT. AXT binding to the protein produced significant alterations in both secondary and tertiary structures of HSA, as revealed from the far-UV and the near-UV CD spectral results. Competitive drug displacement results obtained with phenylbutazone (site I marker), ketoprofen (site II marker) and hemin (site III marker) along with molecular docking results suggested Sudlow's site I, located in subdomain IIA of HSA, as the preferred binding site of AXT.