DFT analysis and in silico exploration of drug-likeness, toxicity prediction, bioactivity score, and chemical reactivity properties of the urolithins

Network pharmacology and molecular docking: combined computational approaches to explore the antihypertensive potential of Fabaceae species

Hypertension is a major global public health issue, affecting quarter of adults worldwide. Numerous synthetic drugs are available for treating hypertension; however, they often come with a higher risk of side effects and long-term therapy. Modern formulations with active phytoconstituents are gaining popularity, addressing some of these issues. This study aims to discover novel antihypertensive compounds in Cassia fistula, Senna alexandrina, and Cassia occidentalis from family Fabaceae and understand their interaction mechanism with hypertension targeted genes, using network pharmacology and molecular docking. Total 414 compounds were identified; initial screening was conducted based on their pharmacokinetic and ADMET properties, with a particular emphasis on adherence to Lipinski's rules. 6 compounds, namely Germichrysone, Benzeneacetic acid, Flavan-3-ol, 5,7,3',4'-Tetrahydroxy-6, 8-dimethoxyflavon, Dihydrokaempferol, and Epiafzelechin, were identified as effective agents. Most of the compounds found non-toxic against various indicators with greater bioactivity score. 161 common targets were obtained against these compounds and hypertension followed by compound-target network construction and protein-protein interaction, which showed their role in diverse biological system. Top hub genes identified were TLR4, MMP9, MAPK14, AKT1, VEGFA and HSP90AA1 with their respective associates. Higher binding affinities was found with three compounds Dihydrokaempferol, Flavan-3-ol and Germichrysone, -7.1, -9.0 and -8.0 kcal/mol, respectively. The MD simulation results validate the structural flexibility of two complexes Flavan-MMP9 and Germich-TLR4 based on no. of hydrogen bonds, root mean square deviations and interaction energies. This study concluded that C. fistula (Dihydrokaempferol, Flavan-3-ol) and C. occidentalis (Germichrysone) have potential therapeutic active constituents to treat hypertension and in future novel drug formulation.

CSC01 shows promise as a potential inhibitor of the oncogenic G13D mutant of KRAS: an in silico approach

About 30% of malignant tumors include KRAS mutations, which are frequently required for the development and maintenance of malignancies. KRAS is now a top-priority cancer target as a result. After years of research, it is now understood that the oncogenic KRAS-G12C can be targeted. However, many other forms, such as the G13D mutant, are yet to be addressed. Here, we used a receptor-based pharmacophore modeling technique to generate potential inhibitors of the KRAS-G13D oncogenic mutant. Using a comprehensive virtual screening workflow model, top hits were selected, out of which CSC01 was identified as a promising inhibitor of the oncogenic KRAS mutant (G13D). The stability of CSC01 upon binding the switch II pocket was evaluated through an exhaustive molecular dynamics simulation study. The several post-simulation analyses conducted suggest that CSC01 formed a stable complex with KRAS-G13D. CSC01, through a dynamic protein-ligand interaction profiling analysis, was also shown to maintain strong interactions with the mutated aspartic acid residue throughout the simulation. Although binding free energy analysis through the umbrella sampling approach suggested that the affinity of CSC01 with the switch II pocket of KRAS-G13D is moderate, our DFT analysis showed that the stable interaction of the compound might be facilitated by the existence of favorable molecular electrostatic potentials. Furthermore, based on ADMET predictions, CSC01 demonstrated a satisfactory drug likeness and toxicity profile, making it an exemplary candidate for consideration as a potential KRAS-G13D inhibitor.

In-vitro and computational analysis of Urolithin-A for anti-inflammatory activity on Cyclooxygenase 2 (COX-2)

Cyclooxygenase 2 (COX-2) participates in the inflammation process by converting arachidonic acid into prostaglandin G2 which increases inflammation, pain and fever. COX-2 has an active site and a heme pocket and blocking these sites stops the inflammation. Urolithin A is metabolite of ellagitannin produced from humans and animals gut microbes. In the current study, Urolithin A showed good pharmacokinetic properties. Molecular docking of the complex of Urolithin A and COX-2 revealed the ligand affinity of -7.97 kcal/mol with the ligand binding sites at TYR355, PHE518, ILE517 and GLN192 with the 4-H bonds at a distance of 2.8 Å, 2.3 Å, 2.5 Å and 1.9 Å. The RMSD plot for Urolithin A and COX-2 complex was observed to be constant throughout the duration of dynamics. A total of 3 pair of hydrogen bonds was largely observed on average of 3 simulation positions for dynamics duration of 500 ns. The MMPBSA analysis showed that active site amino acids had a binding energy of -22.0368 kJ/mol indicating that throughout the simulation the protein of target was bounded by Urolithin A. In-silico results were validated by biological assays. Urolithin A strongly revealed to exhibit anti-inflammatory effect on COX-2 with an IC50 value of 44.04 µg/mL. The anti-inflammatory capability was also depicted through reduction of protein denaturation that showed 37.6 ± 0.1 % and 43.2 ± 0.07 % reduction of protein denaturation for BSA and egg albumin respectively at 500 µg/mL. The present study, suggests Urolithin A to be an effective anti-inflammatory compound for therapeutic use.

Thermal Investigations of Annelated Triazinones-Potential Analgesic and Anticancer Agents

In this article, for the first time, TG-DSC and TG-FTIR investigations of potential pharmaceutics, i.e., analgesic and anticancer active annelated triazinones (1-9) have been presented. The thermal behaviour of these molecules was established in oxidative and inert conditions. The solid-liquid phase transition for each compound (1-9) was documented by one sharp DSC peak confirming the high purity of each sample studied. All the molecules were characterised in terms of calorimetric changes and mass changes during their heating. They revealed high thermal stability in oxidative and inert conditions. The observed tendency in thermal stability changes in relation to a substituent present at the phenyl moiety was found to be similar in air and nitrogen. It was confirmed that annelated triazinones 1-9 were stable up to a temperature range of 241-296 °C in air, and their decomposition process proceeded in two stages under oxidative conditions. In addition, it was established that their thermal stability in air decreased in the following order of R at the phenyl moiety: 4-Cl > 3,4-Cl2 > H > 3-Cl > 4-CH3 > 2-CH3 > 3-CH3 > 2-Cl > 2-OCH3. The volatile decomposition products of the investigated molecules were proposed by comparing the FTIR spectra collected during their thermogravimetric analysis in nitrogen with the spectra from the database of reference compounds. None of annelated triazinones 1-9 underwent any polymorphic transformation during thermal studies. All the compounds proved to be safe for erythrocytes. In turn, molecules 3, 6, and 9 protected red blood cells from oxidative damage, and therefore may be helpful in the prevention of free radical-mediated diseases.

Thermal Decomposition Path-Studied by the Simultaneous Thermogravimetry Coupled with Fourier Transform Infrared Spectroscopy and Quadrupole Mass Spectrometry-Of Imidazoline/Dimethyl Succinate Hybrids and Their Biological Characterization

The thermal decomposition path of synthetically and pharmacologically useful hybrid materials was analyzed in inert and oxidizing conditions for the first time and presented in this article. All the imidazoline/dimethyl succinate hybrids (1-5) were studied using the simultaneous thermogravimetry (TG) coupled with Fourier transform infrared spectroscopy (FTIR) and quadrupole mass spectrometry (QMS). It was found that the tested compounds were thermally stable up to 200-208 °C (inert conditions) and up to 191-197 °C (oxidizing conditions). In both furnace atmospheres, their decomposition paths were multi-step processes. At least two major stages (inert conditions) and three major stages (oxidizing conditions) of their decomposition were observed. The first decomposition stage occurred between T_5% and 230-237 °C. It was connected with the breaking of one ester bond. This led to the emission of one methanol molecule and the formation of radicals capable of further radical reactions in both used atmospheres. At the second decomposition stage (T_max2) between 230-237 °C and 370 °C (inert conditions), or at about 360 °C (oxidizing conditions), the cleavage of the second ester bond and N-N and C-C bonds led to the emission of CH₃OH, HCN, N₂, and CO₂ and other radical fragments that reacted with each other to form clusters and large clusters. Heating the tested compounds to a temperature of about 490 °C resulted in the emission of NH₃, HCN, HNCO, aromatic amines, carbonyl fragments, and the residue (T_max2a) in both atmospheres. In oxidizing conditions, the oxidation of the formed residues (T_max3) was related to the production of CO₂, CO, and H₂O. These studies confirmed the same radical decomposition mechanism of the tested compounds both in inert and oxidizing conditions. The antitumor activities and toxicities to normal cells of the imidazoline/dimethyl succinate hybrids were also evaluated. As a result, the two hybrid materials (3 and 5) proved to be the most selective in biological studies, and therefore, they should be utilized in further, more extended in vivo investigations.

Urolithin A Nanoparticle Therapy for Cisplatin-Induced Acute Kidney Injury

Cisplatin continues to be one of the frontline cytotoxic drugs. However, cisplatin-induced acute kidney injury (AKI) remains a major unmet medical need without any approved pharmacological interventions. The involvement of reactive oxygen species generation and activation of inflammatory and apoptotic pathways in the pathogenesis of cisplatin-induced AKI prompts the use of natural anti-inflammatory compounds. In this context, resolution of inflammation using natural antioxidant and anti-inflammatory such as urolithin A (UA) could prove beneficial. In the end, testing such combinations in models to eliminate the possibility that UA stimulates tumor growth or compromises the potency of cisplatin could prove useful for clinical translation of adjuvant therapies.