Unveiling the Therapeutic Potential of Paclitaxel Combinations Against Breast Carcinoma and Identification of In Vivo Biomarkers.

Breast cancer (BC) is one of the leading causes of high mortality rates in women worldwide. Although advancements have been made in the design of therapeutic strategies and drug discovery, drug resistance remains one of the key challenges. One of the ways to overcome drug resistance is finding potential drug combinations since the efficacy of combined drugs is higher than their individual efficacies if the combination is a synergistic pair. Therefore, the current study uses a BC patient-derived xenograft (PDX) dataset to evaluate the effects of various cancer drugs on breast cancer in vivo models. The drug effects are further validated by four machine learning models, namely Elastic Net, Least Absolute Shrinkage and Selection (LASSO), Support Vector Machine (SVM), Random Forests (RF), as well as exploring the shortlisted drugs in combination with paclitaxel, a baseline drug for enhanced efficacy on tumor volume reduction. Additionally, the study also shortlists the top 50 in vivo biomarkers correlated with the effects of the drugs. The outcomes could be significantly important for the design of an effective anti-breast cancer therapy.

Experimental and Computational Investigation on the Interaction of Anticancer Drug Gemcitabine with Human Plasma Protein: Effect of Copresence of Ibuprofen on the Binding.

The interaction of common anticancer drug gemcitabine with human serum albumin (HSA) has been studied in detail. The effect of an omnipresent nonsteroidal anti-inflammatory drug ibuprofen was also seen on the binding of HSA and gemcitabine. A slight hyperchromic shift in the difference UV-visible absorption spectra of HSA on the addition of gemcitabine gave a primary idea of the possible complex formation between them. The inner filter effect, which happens due to the significant absorbance of the ligand at the excitation and/or emission wavelengths, played an important role in the observed fluorescence quenching of HSA by gemcitabine that can be understood by comparing the observed and corrected fluorescence intensities obtained at λex = 280 nm and 295 nm. Gemcitabine showed weak interaction with HSA, which took place via a dynamic quenching mechanism with 1:1 cooperative binding between them. Secondary structural analysis, based on circular dichroism (CD) spectroscopy, showed that low concentrations of gemcitabine did not affect the native structure of protein; however, higher concentrations affected it slightly with partial unfolding. For understanding the binding site of gemcitabine within HSA, both experimental (using site markers, warfarin and ibuprofen) as well as computational methods were employed, which revealed that the gemcitabine binding site is located between the interface of subdomain IIA and IIB within the close proximity of the warfarin site (drug site 1). The effect of ibuprofen on the binding was further elaborated because of the possibility of its coexistence with gemcitabine in the prescription given to the cancer patients, and it was noticed that, ibuprofen, even present in high amounts, did not affect the binding efficacy of gemcitabine with HSA. DFT analyses of various conformers of gemcitabine obtained from its docking with various structures of HSA (free and bounded with site markers), show that the stability of the gemcitabine molecule increased slightly after binding with ibuprofen-complexed HSA. Both experimental as well as computational results were in good agreement with each other.

Biophysical binding profile with ct-DNA and cytotoxic studies of a modulated nanoconjugate of umbelliferone cobalt oxide loaded on graphene oxide (GO) as drug carrier.

In an attempt to identify suitable nano-carriers for drug delivery, natural drug umbelliferone was chosen to synthesize new modulated nanoconjugate of umbelliferone cobalt oxide with cobalt (II) nitrate in one pot assembly in the presence of tannic acid. The synthesized nanoconjugate drug (NCD) was then loaded on graphene oxide (GO) as drug carrier by simple ultrasonication method and thoroughly characterized by various spectroscopic techniques (FT-IR, SEM, TEM, XRD, EPR and thermogravimetric analysis) which revealed the successful loading of the nanoconjugate drug on GO. The UV-visible, fluorescence and electrochemical studies suggested that strong π-π stacking interactions exist between nanoconjugate drug and GO. The binding studies of NCD-GO with ct-DNA were performed by various optical and biophysical methods viz., UV-visible, fluorescence, circular dichroism (CD) and cyclic voltammetry (CV) which indicated electrostatic mode of binding towards the ct-DNA. Furthermore, condensate of nanoconjugate drug-loaded GO (NCD-GO) with ct-DNA was prepared and analyzed by scanning electron microscopy (SEM) which revealed that the interaction of NCD-GO with ct-DNA had occurred. Cleavage activity of NCD-GO with pBR322 was evaluated by gel electrophoresis and it was found that NCD-GO cleave DNA through hydrolytic pathway involving hydroxyl radical (OH). The cytotoxicity of NCD-GO was evaluated against human liver carcinoma (Huh-7), prostate cancer (Du-145) cell lines along with normal cell line (PNT 2). The results obtained showed selective cytotoxic activity of NCD-GO against Du-145 cell lines. The intracellular uptake was visualized by confocal microscopy which revealed the significant cellular uptake and internalization of nanoparticles by cells. Moreover, the adsorption of cobalt oxide umbelliferone on GO was studied by density functional theory. The process of adsorption was found exothermic in nature and the optimized geometry structure is quite stable. Communicated by Ramaswamy H. Sarma.

Experimental and computational investigation on the binding of anticancer drug gemcitabine with bovine serum albumin.

This study reports the experimental and computational investigation on the binding of a common anticancer drug, gemcitabine, with the model plasma protein, bovine serum albumin (BSA). Several experimental and computational methods, such as intrinsic and synchronous fluorescence, UV-visible, and circular dichroism spectroscopies, consensus molecular docking and molecular dynamics simulation have been employed to elucidate the binding mechanism. Gemcitabine altered the UV-visible spectrum of BSA, which is a clear indication of the complex formation between them. The visual inspection of observed fluorescence quenching results at λex = 280 nm and 295 nm has shown the substantial involvement of tyrosine residue, even larger than tryptophan. However, after the correction of inner filter effect of the observed data, it became clear that tyrosine has a negligible role in quenching. A 20-fold decrease in quenching constant was found in the corrected data, as compared to the observed data at λex = 280 nm. There was a 1:1 weak binding between BSA and gemcitabine accompanied by dynamic quenching. The secondary structure of BSA remained almost intact in the presence of gemcitabine. The primary binding site of gemcitabine inside BSA was the drug binding site 2 or DS II, which is located in the subdomain 3 A. MD Simulation results suggested that gemcitabine doesn't affect or deviate the structure of BSA upon interaction throughout 100 ns time period. The dominating intermolecular forces were hydrophobic forces and hydrogen bonding. A small change in the frontier molecular orbitals of gemcitabine was also observed after its binding with BSA.Communicated by Ramaswamy H. Sarma.

Noncovalent molecular interactions between antineoplastic drug gemcitabine and a carrier protein identified through spectroscopic and in silico methods.

Herein we have studied the noncovalent molecular interactions between hen egg white lysozyme (HEWL) and the commonly employed antineoplastic drug gemcitabine through the cumulative implementation of spectroscopic techniques and in silico approaches. The formation of a complex between HEWL and gemcitabine was made evident by the differences between the UV-visible spectra of the protein and protein-gemcitabine complex. Fluorescence quenching of HEWL by gemcitabine was hardly detectable at room temperature, but it became prominent at higher temperatures. Very low values for the bimolecular quenching constant and the non-reciprocal dependence of quenching on temperature indicated that dynamic quenching was taking place. Analysis of experimental data indicated that the interaction was dominated by hydrophobic forces, while the results of a computational investigation suggested the concomitant contribution of hydrogen bonding. Gemcitabine binding induced modifications of the secondary structure of HEWL by slightly increasing the α-helical content of the protein. Finally, gemcitabine binding site was inferred to be located in HEWL big hydrophobic cavity.

Fluorescent delivery vehicle containing cobalt oxide-umbelliferone nanoconjugate: DNA/protein interaction studies and anticancer activity on MF7 cancer cell line.

Fluorescent labeling is limited to certain molecules and alters biomolecule functionality. A new class of nanomaterial with anticancer activity and fluorescence properties has been designed and prepared. This nanotherapeutic conjugate of natural molecules has a selective binding site in cancer cell lines. Natural drug umbelliferone was taken with cobalt metal ions in a one pot assembly in the presence of tannic acid which yields new fluorescent nanoparticles of umbelliferone cobalt oxide nanoconjugate. Umbelliferone has high fluorescent properties and also has coordination ability to bind with central metal ions. The nanoconjugate was synthesized and characterized by using TEM, EDX analysis, SEM, XRD, and FTIR spectroscopy. TEM shows that the average size of the particles formed with umbelliferone is ∼20 nm. The solubility of the drug nanoparticles in water showed compatibility with cancer cells and provided a favorable environment to investigate the mechanism of action on the MCF-7 cell line. The nanoconjugate is microcrystalline in nature and gives a clear suspension in water. The nanocobalt conjugate was loaded on TiO2 nanoparticles by ultrasonication, and the solution was digested overnight. The conjugate of the drug with a TiO2 drug carrier was stable in solution and maintained the nanostructure ∼34.6 nm. A comparative study with nano-vehicle TiO2 and the nanoconjugate was performed. TiO2 was used to compare the anti-cancer activity of the nanoconjugate at low dose in vitro. It was observed that the nanoconjugate with TiO2 is capable of reaching the specific target like the TiO2 nanoparticle and enhance the chemotherapeutic impact. Hence, the nanoconjugate can also be used like nano-TiO2, as the drug and carrier. The ct-DNA and HSA protein binding studies were done and validated by docking studies.

Spectroscopic and computational evaluation on the binding of safranal with human serum albumin: Role of inner filter effect in fluorescence spectral correction.

For determining the pharmacological properties of medicinal compounds, their binding with serum albumins is very crucial. Herein, we have selected safranal, a major constituent of saffron which is known to retain a number of medicinal properties including antioxidant, anti-inflammatory, tumoricidal, anti-genotoxic, and anti-aging activities; and studied its mechanism of binding with human serum albumin at physiological pH using various spectroscopic methods along with computational approach using molecular docking. A change in the difference UV-visible spectrum of HSA in presence of safranal was found which is due to the complex formation. Owing to the strong absorption of safranal at the fluorescence excitation wavelength of HSA (295 nm) and in the whole range of emission, the fluorescence spectra of HSA in presence of safranal were corrected for the inner filter effect. After the correction the spectra were free from the safranal absorption effect and it was found that addition of safranal causes the quenching of HSA fluorescence and a blue shift of the emission maximum which are attributed to the binding of safranal to the protein and dominance of hydrophobic forces in the interaction, respectively. It was evident from the comparison of observed and corrected fluorescence spectra that before correction there was a large red shift while after correction appearance of blue shift was occurred. The involvement of hydrophobic interaction was also found from the extrinsic fluorescence measurements using ANS dye as well as from the analyzed thermodynamic parameters. Safranal was found to partially induce the secondary structure of HSA as construed from the CD measurements. The size of the HSA was also decreased as evident from the DLS and RLS measurements. Both site marker studies and molecular docking simulations suggested that the primary binding site of the safranal in the HSA is Sudlow's site 1 located in the subdomain IIA. Hydrophobic interaction provides the major contribution to the binding forces along with a little amount of hydrogen bonding.

Human serum albumin binding to the biologically active labdane diterpene "leoheterin": Spectroscopic and in silico analysis.

Labdane diterpenes are important substances due to their remarkable biological activities such as, antibacterial, antiprotozoal, antifungal and cytostatic and cytotoxic effects against human cancer cells. We have isolated a labdane diterpene named "leoheterin" from the aerial parts of the Otostegia fruticosa Forssk (Briq) obtained from south west Arabian mountains of Saudi Arabia. The isolated compound was characterized by 1HNMR, 13CNMR, IR and UV-visible spectroscopies. Due to the pharmaceutical importance of this class of compounds we have studied the interaction of HSA with leoheterin by using several spectroscopic methods. The change in the UV spectrum of HSA in presence of leoheterin gives a primary idea about the interaction between them. Congruently, leoheterin quenches the fluorescence of HSA with a prominent blue shift of 5 nm, reminiscent of involvement of hydrophobic interactions. There was 1:1 binding between leoheterin and albumin which was taken place via static quenching mechanism. From CD it was revealed that leoheterin induces the secondary structure of HSA which is further supported by 3-d fluorescence measurements which shows a decrease in the size of the HSA-leoheterin complex as compared to the HSA alone. Molecular docking simulations presented that among the first three conformers, which have been arranged according to the least binding energies and are also in good corroboration with the free energies of binding obtained experimentally, the first two conformers shown the binding in hemin binding site of subdomain IB while in third conformer the binding site was near to the drug binding site 1 located in subdomain IIA. All conformers exhibited the involvement of hydrogen bonding as well as hydrophobic interactions.

Comprehensive exploration of the anticancer activities of procaine and its binding with calf thymus DNA: a multi spectroscopic and molecular modelling study.

Procaine is an anesthetic drug commonly administrated topically or intravenously for use in local anesthesia. Promisingly, some anticancer activities of procaine have also been reported. Therefore, the mechanism of interaction between anesthetic drug procaine with ct-DNA was determined collectively by means of various spectroscopic and molecular docking methods. Minor groove 1 : 1 binding of procaine to the ct-DNA was evidenced from absorption spectroscopy, fluorescence quenching, DNA melting, competitive binding measurements with EB and DAPI dyes, viscosity and CD spectroscopy together with molecular docking simulations and DFT calculations. Molecular docking on five different B-DNA structures (taken from the Protein Data Bank) shows that procaine binds in the AT rich region of all five B-DNA structures. Thermodynamic parameters, evaluated using van't Hoff's isotherm, shown that the interaction was feasible and the binding forces involved were hydrophobic as well as hydrogen bonding which were, further, confirmed by molecular docking. The frontier molecular orbitals (HOMO and LUMO) of procaine and DNA bases have been calculated by DFT method and the chemical potential (µ), chemical hardness (η) and fraction number of electrons (ΔN) from procaine to DNA bases were evaluated, which have shown that procaine acts as an electron donor to the DNA bases. Simultaneously, anticancer activities of procaine alone and in combination with doxorubicin were observed on the MCF-7 breast cancer cell line. The results showed that the combined treatment with both procaine and doxorubicin enhanced the cytotoxic and apoptotic inducing potential of doxorubicin.

Elucidation of the interaction of human serum albumin with anti-cancer sipholane triterpenoid from the Red Sea sponge.

A sipholane triterpenoid, named sipholenone A, with anti-cancer properties was isolated from the Red Sea sponge Siphonochalina siphonella and characterized by proton and carbon-13 nuclear magnetic resonance (1 H NMR and 13 C NMR) spectroscopies. The goal of this study was to visualize the binding of this triterpenoid with human serum albumin (HSA) and to determine its binding site on the biomacromolecule. The interaction was visualized using fluorescence quenching, synchronous fluorescence, far- and near-UV circular dichroism (CD), UV-visible and Fourier transform-infrared (FT-IR) spectroscopies. UV-visible spectroscopy indicated the formation of a ground-state complex as a result of the interaction. Sipholenone A quenches the fluorescence of HSA via a static quenching mechanism. A small blue shift in the fluorescence quenching profiles suggested the involvement of hydrophobic forces in the interaction. Sipholenone A binding takes place at site I of subdomain II A with a 1:1 binding ratio, as revealed by displacement binding studies using warfarin, ibuprofen and digitoxin. Far-UV CD and FT-IR studies showed that the binding of sipholenone A to HSA also had a small effect on the protein's secondary structure with a slight decrease in the α-helical content. Several thermodynamic parameters were calculated, along with Forster's radiative energy transfer analysis.

Mucoadhesive microparticulate drug delivery system of curcumin against Helicobacter pylori infection: Design, development and optimization.

The purpose of the present research was to develop and characterize mucoadhesive microspheres of curcumin for the potential use of treating gastric adenocarcinoma, gastric and duodenal ulcer associated with Helicobacter pylori. Curcumin mucoadhesive microspheres were prepared using ethyl cellulose as a matrix and carbopol 934P as a mucoadhesive polymer by an emulsion-solvent evaporation technique. Response surface methodology was used for optimization of formulation using central composite design (CCD) for two factors at three levels each was employed to study the effect of independent variables, drug:polymer:polymer ratio (curcumin:ethylcellulose:carbopol 934P)(X1) and surfactant concentration (X2) on dependent variables, namely drug entrapment efficiency (DEE), percentage mucoadhesion (PM), in vitro drug release and particle size (PS). Optimized formulation was obtained using desirability approach of numerical optimization. The experimental values of DEE, PM, % release and PS after 8 h for the optimized formulation were found to be 50.256 ± 1.38%, 66.23%±0.06, 73.564 ± 1.32%, and 139.881 ± 2.56 µm, respectively, which were in close agreement with those predicted by the mathematical models. The drug release was also found to be slow and extended more than 8 h and release rates were fitted to the Power law equation and Higuchi model to compute the diffusional parameters. The prolonged stomach residence time of curcumin mucoadhesive microspheres might make a contribution to H. pylori complete eradication in combination with other antimicrobial agents.

Unfolding of rabbit serum albumin by cationic surfactants: surface tensiometry, small-angle neutron scattering, intrinsic fluorescence, resonance Rayleigh scattering and circular dichroism studies.

Unfolding of rabbit serum albumin (RSA) by cationic surfactants cetyltrimethylammonium bromide (CTAB) and tetradecyltrimethylammonium bromide (TTAB) was studied by exploiting surface tensiometry, small-angle neutron scattering (SANS), intrinsic fluorescence, resonance Rayleigh scattering (RRS) (also referred as turbidity at 350/350), and circular dichroism (CD) techniques. Surface tension measurements revealed the formation of highly surface-active complexes occurring as a consequence of RSA-surfactants interactions. SANS measurements show that, in the low surfactant concentration regime (0-10 mM), increase in the dimension of the ellipsoidal protein occurs. Conversely, at higher concentrations (20-80 mM), the surfactant molecules result in the formation of a fractal structure representing a 'necklace model' of micelle-like clusters randomly distributed along the polypeptide chain. The overall size of the complex increases and the fractal dimension decreases on increasing the surfactant concentration. The size of the micelle-like clusters decreases while the number of such clusters and their aggregation number increase with increasing CTAB concentration. Taken all observant together, the fluorescence, RRS, and CD studies were found to be consistent with the SANS measurements. Both CTAB and TTAB were found to behave likewise and the effect of hydrophobicity was clearly visible in the CD, RRS, and intrinsic fluorescence results. The Rayleigh scattering study shows that TTAB was more skilled to solubilize the serum albumin and may be more convenient than CTAB to isolate proteins from inclusion bodies.

Multi-technique approach on the effect of surfactant concentrations on the thermal unfolding of rabbit serum albumin: formation and solubilization of the protein aggregates.

Effect of cationic surfactant, cetyltrimethylammonium bromide (CTAB) addition on the thermal denaturation of rabbit serum albumin (RSA) has been studied by employing small-angle neutron scattering (SANS), circular dichroism (CD), intrinsic fluorescence and ultra violet (UV) spectroscopy. The studies were performed at three different temperatures viz., 30, 50 and 70 degrees C and at two different concentrations of CTAB: the low concentration of CTAB used was 1mM and the higher concentration was 80 mM (for SANS) and 20mM (for CD, fluorescence and UV). A collective effect of high temperature and low concentration of CTAB led to the protein aggregation followed by solubilization of these aggregates at higher concentration of surfactant. At 1mM CTAB and 30 degrees C, the protein-surfactant complex has a prolate ellipsoidal shape with semi-major axis of 88.9A and semi-minor axis of 19.6A which are slightly greater than the values of the native RSA. At 50 degrees C, the size of the semi-major axis increases while at 70 degrees C an increase in the size of both axes was found. The thermal outcome at higher concentration of CTAB (80 mM) was rather different. Higher concentration of CTAB unfolds the protein by the formation of micelle-like aggregates along the polypeptide chains of the protein and the complex was stabilized at higher temperatures, which was not found with lower concentration of CTAB. The CD results were found to be consistent with the SANS results, i.e., decrease in alpha-helicity of RSA was more when less amount of surfactant was present as compared to the system with higher surfactant concentration. In a similar fashion, results of relative fluorescence intensity (RFI) reveal that increase in temperature causes decrease in lambda(max) of native RSA as well as RSA+1mM CTAB, whereas the lambda(max) remains unchanged for RSA+20mM CTAB systems. That means the structure remains compact in presence of 20mM CTAB while the structure becomes loose when low or zero amount of surfactant was present. The UV results indicate that the protein aggregation takes place in presence of low amount of CTAB and these aggregates become soluble at high concentration of CTAB.

Amphiphilic drug persuaded collapse of polyvinylpyrrolidone and poly(ethylene glycol) chains: a dynamic light scattering study.

Light scattering has proved to be useful in characterizing colloidal systems. We have studied the interaction between an amphiphilic drug, amitriptyline hydrochloride (AMT), and neutral polymers, polyvinylpyrrolidone (PVP) and poly(ethylene glycol) (PEG), using the dynamic light scattering (DLS) technique. AMT was found to interact with PVP more strongly than PEG. A large decrease of the size of aggregates upon increase of AMT concentration indicates a successive collapse of the polymer conformation. The partial negatively charged oxygen atoms, present in the amide group of PVP, were believed to be responsible for the collapse while interacting with the cationic head group of AMT. Presence of NaBr in the solution enhanced the effect markedly and made the AMT-PVP aggregates more compact. The PEG aggregates also showed a similar behavior, although less pronounced than the PVP. The results obtained in the present investigations may be helpful to design the drug delivery systems for the antidepressant drugs as the higher concentration of these drugs is harmful for the human body. Likewise, as the results have shown that on increasing the temperature there is a decrease in the extent of interaction; this may be helpful for the controlled release formulations.