Identification of indole-based natural compounds as inhibitors of PARP-1 against triple-negative breast cancer: a computational study

Triple-negative breast cancer (TNBC) is the most aggressive kind of breast cancer known to mankind. It is a heterogeneous disease that is formed due to the missing estrogen, progesterone and human epidermal growth factor 2 receptors. Poly(ADP-ribose) polymerase-1 (PARP-1) protein helps in the development of TNBC by repairing the cancer cells, which proliferate and spread metastatically. To determine the potential PARP-1 inhibitors (PARPi), 0.2 million natural products from Universal Natural Product Database were screened using molecular docking and six hit compounds were selected based on their binding affinity towards PARP-1. The bio-availability and drug-like properties of these natural products were evaluated using ADMET analysis. Molecular dynamics simulations were conducted for these complexes for 200 ns to examine their structural stability and dynamic behaviour and further compared with the complex of talazoparib (TALA), an FDA-approved PARPi. Using MM/PBSA calculations, we conclude that the complexes HIT-3 and HIT-5 (-25.64 and -23.14 kcal/mol, respectively) show stronger binding energies with PARP-1 than TALA with PARP-1 (-10.74 kcal/mol). Strong interactions were observed between the compounds and hotspot residues, Asp770, Ala880, Tyr889, Tyr896, Ala898, Asp899 and Tyr907, of PARP-1 due to the existence of various types of non-covalent interactions between the compounds and PARP-1. This research offers critical information about PARPi, which could potentially be incorporated into the treatment of TNBC. Moreover, these findings were validated by comparing them with an FDA-approved PARPi.

Discovery of novel HDAC8 inhibitors from natural compounds by in silico high throughput screening

A class I histone deacetylase HDAC8 is associated with several diseases, including cancer, intellectual impairment and parasite infection. Most of the HDAC inhibitors that have so far been found to inhibit HDAC8 limit their efficacy in the clinic by producing toxicities. It is therefore very desirable to develop specific HDAC8 inhibitors. The emergence of HDAC inhibitors derived from natural sources has become quite popular. In recent decades, it has been shown that naturally occurring HDAC inhibitors have strong anticancer properties. A total of 0.2 million natural compounds were screened against HDAC8 from the Universal Natural Product Database (UNPD). Molecular docking was performed for these natural compounds and the top six hits were obtained. In addition, molecular dynamics (MD) simulations were used to evaluate the structural stability and binding affinity of the inhibitors, which showed that the protein-ligand complexes remained stable throughout the 100 ns simulation. MM-PBSA method demonstrated that the selected compounds have high affinity towards HDAC8. We infer from our findings that Hit-1 (-29.35 kcal mol-1), Hit-2 (-29.15 kcal mol-1) and Hit-6 (-30.28 kcal mol-1) have better binding affinity and adhesion to ADMET (absorption, distribution, metabolism, excretion and toxicity) characteristics against HDAC8. To compare our discussions and result in an effective way. We performed molecular docking, MD and MM-PBSA analysis for the FDA-approved drug romidepsin. The above results show that our hits show better binding affinity than the compound romidepsin (-12.03 ± 4.66 kcal mol-1). The important hotspot residues Asp29, Ile34, Trp141, Phe152, Asp267, Met274 and Tyr306 have significantly contributed to the protein-ligand interaction. These findings suggest that in vitro testing and additional optimization may lead to the development of HDAC8 inhibitors.Communicated by Ramaswamy H. Sarma.

Design of Ascorbic Acid Eutectic Mixtures With Sugars to Inhibit Oxidative Degradation

L-Ascorbic acid (ASC), commonly known as vitamin C, acts as an anti-oxidant in the biological system. It is extensively used as an excipient in pharmaceutical industry, food supplements in fruit juices, and food materials due to its free radicals scavenging activity. Main drawback of ASC is its poor aqueous stability owing to the presence of lactone moiety that is easily oxidized to dehydroascorbic acid and further degraded. To improve aqueous stability and inhibit oxidative degradation, ASC was co-crystallized to constitute binary eutectic compositions with mono and di-saccharides such as glucose, sucrose, lactose, and mannitol. The eutectics were confirmed by their (single) lower melting endotherm compared to ASC and sugars, although Powder X-ray diffraction (PXRD) and Fourier transform Infrared spectroscopy (FT-IR) data confirmed the characteristics of their physical mixture. Scanning electron microscope (SEM) images of the binary eutectics confirmed their irregular morphology. The ASC eutectics exhibited improved shelf-life by 2–5-fold in weakly acidic (pH 5) and neutral (pH 7) aqueous buffer medium, whereas the eutectic with glucose enhanced shelf-life only by 1.1–1.2-fold in acidic medium (pH 3.3 and 4). Notably, stabilizing effect of the sugar eutectics decreased with increasing acidity of the medium. In addition, higher binding energy of the disaccharide eutectics partially supports the aqueous stability order of ASC in the neutral pH medium due to more number of non-bonded interactions than that of monosaccharides.

Antiviral activities of natural compounds and ionic liquids to inhibit the Mpro of SARS-CoV-2: a computational approach

The recalcitrant spread of the COVID-19 pandemic produced by the novel coronavirus SARS-CoV-2 is one of the most destructive occurrences in history. Despite the availability of several effective vaccinations and their widespread use, this line of immunization often faces questions about its long-term efficacy. Since coronaviruses rapidly change, and multiple SARS-CoV-2 variants have emerged around the world. Therefore, finding a new target-based medication became a priority to prevent and control COVID-19 infections. The main protease (Mpro) is a salient enzyme in coronaviruses that plays a vital role in viral replication, making it a fascinating therapeutic target for SARS-CoV-2. We screened 0.2 million natural products against the Mpro of SARS-CoV-2 using the Universal Natural Product Database (UNPD). As well, we studied the role of ionic liquids (ILs) on the structural stabilization of Mpro. Cholinium-based ILs are biocompatible and used for a variety of biomedical applications. Molecular docking was employed for the initial screening of natural products and ILs against Mpro. To predict the drug-likeness features of lead compounds, we calculated the ADMET properties. We performed MD simulations for the selected complexes based on the docking outcomes. Using MM/PBSA approaches, we conclude that compounds NP-Hit2 (-25.6 kcal mol-1) and NP-Hit3 (-25.3 kcal mol-1) show stronger binding affinity with Mpro. The hotspot residues of Thr25, Leu27, His41, Met49, Cys145, Met165, and Gln189 strongly interacted with the natural compounds. Furthermore, naproxenate, ketoprofenate, and geranate, cholinium-based ILs strongly interact with Mpro and these ILs have antimicrobial properties. Our findings will aid in the development of effective Mpro inhibitors.

Carbon dioxide adsorption and activation on ionic liquid decorated Au(111) surface: A DFT study

We use first principle approaches to study the adsorption and catalytic activation mechanism of CO₂ on ionic liquids (ILs, [C_nMIm]⁺[Cl]^- (n = 0-6)) attached to a Au(111) surface. The adsorption of CO₂ at this liquid-solid model interface occurs via either (i) parallel π-stacking mode or (ii) CO₂ oxygen lone pair (lp)···π interaction. These CO₂ physisorption modes, which depend on the CO₂ landing angle at this interface, are identified as an efficient way to activate CO₂ and its further conversion into value-added products. For illustration, we discuss the conversion of CO₂ into formic acid where the ILs@Au(111) decorated interface allows reduction of the activation energy for the CO₂ + H₂ → HCOOH reaction. In sum, our electrode/electrolyte based interface model provides valuable information to design novel heterogeneous catalysts for CO₂ conversion. Indeed, our work establishes that a suitable interface material is enough to activate CO₂.

The molecular mechanism behind the stabilization of insulin by choline and geranate (CAGE) ionic liquids - computational insights into oral insulin drug formulation

Insulin is a principal hormone that is involved in the regulation of glucose levels in the blood. Oral insulin formulation is a recent development in drug delivery systems. Biocompatible choline-based ionic liquids (ILs) show promising antibacterial activity and are useful for oral and transdermal drug delivery applications. Choline and geranate (CAGE) ILs enhance the stability and oral efficacy of insulin delivery. The molecular mechanism behind insulin formulation in the oral form is at issue. In the present work, the molecular-level understanding of CAGE ILs in insulin is scrutinized by employing atomistic molecular dynamics (MD) simulations. To identify the stability of insulin in an IL medium, we have studied a series of concentration (mole fraction 0.05-1.00) of CAGE ILs with an insulin dimer. It can be well evidenced from the experimental reports that in an aqueous medium, there is a refashioning of CAGE nanostructures at 0.50 mole fraction. It is found from our calculations that the first solvation shell of insulin is readily occupied by choline and geranate ions in the presence of water. Moreover, the geranate ions strongly interacted with the water molecules and thereby, eliminating the intermolecular hydrogen bonding (H-bonding) interactions towards the insulin at 0.30-0.50 mole fraction of CAGE ILs. The most desirable 0.30-0.50 mole fraction of CAGE invigorates water-mediated H-bonding interactions with geranate ions, which also enhances the electrostatic behavior around the vicinity of the insulin dimer. These important findings can help in the development of oral insulin drug delivery and related applications.

The effect of DTPA on calcium carbonate scale deposition on copper and aluminium surfaces

Calcium carbonate (CaCO₃) scale inhibition by Diethylenetriaminepentaacetic acid (DTPA) on copper and aluminium metal surfaces was studied at 60 and 100 °C. The samples were characterized using X-ray diffraction (XRD), Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The results revealed a novel pot like morphology for calcite which was resulted from the transformation of dumbbell morphology. The pot like morphology exposed the possibility of hollow structures for other polymorphs and is resulted from the breaking apart of the dumbbell structures at the middle, followed by fluffing of the separated parts.

Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids

The hydrated clusters of protonated imidazole (ImH⁺) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.

Experimental investigation on convective heat transfer and pressure drop of cone helically coiled tube heat exchanger using carbon nanotubes/water nanofluids

This study investigates the heat transfer and the pressure drop of cone helically coiled tube heat exchanger using (Multi wall carbon nano tube) MWCNT/water nanofluids. The MWCNT/water nanofluids at 0.1%, 0.3%, and 0.5% particle volume concentrations were prepared with the addition of surfactant by using the two-step method. The tests were conducted under the turbulent flow in the Dean number range of 2200 < De < 4200. The experiments were conducted with experimental Nusselt number is 28%, 52% and 68% higher than water for the nanofluids volume concentration of 0.1%, 0.3% and 0.5% respectively. It is found that the pressure drop of 0.1%, 0.3% and 0.5% nanofluids are found to be 16%, 30% and 42% respectively higher than water. It is studied that the prepared MWCNT/water nanofluids show good stability even after 45 days of preparation and there is no considerable deposit of nanotubes on the tube inner wall. It is also studied that there is no immediate risk of handling MWCNT and studied that there is no significant erosion of coiled tube inner wall surface even after several test runs. Therefore the MWCNT/water nanofluids are the alternate heat transfer fluids for traditional fluids in the cone helically coiled tube heat exchanger to improve the heat transfer with considerable pressure drop.

Preparation, Characterization and Evaluation of Elvitegravir-Loaded Solid Lipid Nanoparticles for Enhanced Solubility and Dissolution Rate

Purpose: To enhance the aqueous solubility and dissolution rate of elvitegravir (EVG) by formulating the drug as solid lipid nanoparticles (SLNs) using solvent injection method.Methods: EVG-loaded SLNs were prepared by solvent injection method. Four different formulations of SLN were prepared using gelucire - 44/14 as lipid core in ethanol, soya lecithin as emulsifier, and polysorbate 80 as surfactant in the aqueous phase. The SLNs were characterized for various physical properties, including particle size, zeta potential, polydispersity, release profile and entrapment efficiency.Results: The yield of SLNs was in the range 151.0 ± 2.4 to 199.1 ± 2.7 nm. Significant changes were observed in mean particle size (nm), Z - potential (mV) and polydispersity index (PDI) of the SLNs by varying the  concentration of cryoprotectant. EVG – SLNs demonstrated a 800 – 1030-fold enhancement in aqueous solubility compared with plain EVG. The dissolution efficiency (DE) for SLNs was > 63 % in all cases and increased up to 83 % with increasing lipid load.Conclusion: Successful preparation and characterization of elvitegravir–loaded solid lipid nanoparticles by solvent injection method has been accomplished in this study.Keywords: Elvitegravir, Solid lipid nanoparticles, Cryoprotectant, Lipid load, Entrapment efficiency