Bioactive compounds from Pandanous fascicularis as potential therapeutic candidate to tackle hepatitis a inhibition: Docking and molecular dynamics simulation study

Explicit water-ligand docking, drug-likeness and molecular dynamics simulation analysis to predict the potency of Boerhavia diffusa plant extract against mutant wilms tumor-1 protein responsible for type 4 nephrotic syndrome

Thestructure and function of a protein are closely connected. Changes in a protein structure can impact on its function. Nephrotic syndrome type 4 (NPHS4) is an uncommon genetic condition caused by mutations in the WT1 gene, which codes for the wilms tumor-1 protein. Several studies have discovered that patients with nephrotic syndromes are resistant to steroid therapy and are likely to develop end-stage renal failure. The use of phytochemicals-based therapeutics is in demand due to their high potential and low toxicity. Based on this context, we employed the Autodock raccoon to screen 67 distinct potent phytochemicals from the Boerhavia diffusa (B.diffusa) plant against the wild type and mutant model at position C388R (cysteine is replaced with arginine at position 388) of the C-terminal DNA binding domain of the wilms tumor-1 protein. Out of 67 active compounds, only 10 compounds (lunamarine, kaempferol, boeravinone B, boeravinone E, boeravinone A, boeravinone F, boeravinone J, boeravinone P, boerhaavic acid and 4',7-dihydroxy-3'-methylflavone) were screened based on drug-likeness properties and binding energy for explicit water ligand docking against wild and mutant model of C-terminal DNA binding domain of wilms tumor-1 protein. Consequently, the hydrated form of boeravinone F and boeravinone A demonstrated the highest binding energy against the protein mutant model described above, the binding energies were -9.56 and -8.96 Kcal/mol, respectively. Followed by explicit water ligand docking the microscopic properties of wild type, mutant, mutant-boeravinone F complex, and mutant-boeravinone A complex systems were evaluated using molecular dynamics simulation steps with 100 ns of trajectory. The findings indicate that, due to mutation the mutant model system had decreasing stability and decreasing compactness nature. However, boeravinone A effectively monitored the mutant system's stability and improved compactness nature after binding with the mutant model. Boeravinone A with the mutant model complex system was determined to have the lowest energy point as compared to other studied systems. The study revealed minimal structural alterations and reduced conformational mobility.

Computational pharmacology profiling of borapetoside C against melanoma

Melanoma,also known as a 'black tumor', begins in the melanocytes when cells (that produce pigment) grows out of control. Immunological dysregulation, which raises the risk for multiple illnesses, including melanoma, may be influenced by stress tiggered through viral infection, long term effects of ultraviolet radiation, environmental pollutants etc. Borapetoside C is one of the phytoconstituents from Tinospora crispa, and its biological source has been reported for its antistress property. Network pharmacology and KEGG pathway analysis of borapetoside C-regulated proteins were conducted to identify the hub genes involved in melanoma development. Further, a molecular docking was performed between borapetoside C and targets involved in melanoma. Further, the top 3 complexes were selected based on the binding energy to conduct molecular dynamics simulations to evaluate the stability of ligand-protein complex followed by principal component analysis and dynamic cross-correlation matrix. In addition, borapetoside C was also screened for its pharmacokinetics and toxicity profile. Network Pharmacology studies and KEGG pathway analysis revealed 8 targets involved in melanoma. Molecular docking between borapetoside C and targets involved in melanoma identified 3 complexes with minimum binding i.e. borapetoside C- MAP2K1, MMP9, and EGFR. Further, molecular dynamics simulations showed a stable complex of borapetoside C with MMP9 and EGFR. The present study suggested that borapetoside C may target MMP9 and EGFR to possess an anti-melanoma property. This finding can be useful in developing a novel therapeutic agent against melanoma from a natural source.Communicated by Ramaswamy H. Sarma.

Identification of novel AKT1 inhibitors from Sapria himalayana bioactive compounds using structure-based virtual screening and molecular dynamics simulations

Through the experimental and computational analyses, the present study sought to elucidate the chemical composition and anticancer potential of Sapria himalayana plant extract (SHPE). An in vitro analysis of the plant extract was carried out to determine the anticancer potential. Further, network pharmacology, molecular docking, and molecular dynamic simulation were employed to evaluate the potential phytochemical compounds for cervical cancer (CC) drug formulations. The SHPE exhibited anti-cancerous potential through inhibition properties against cancer cell lines. The LC-MS profiling showed the presence of 14 compounds in SHPE. Using network pharmacology analysis, AKT1 (AKT serine/threonine kinase 1) is identified as the possible potential target, and EGFR (Epidermal Growth Factor Receptor) is identified as the possible key signal pathway. The major targets were determined to be AKT1, EGFR by topological analysis and molecular docking. An in silico interaction of phytoconstituents employing molecular docking demonstrated a high binding inclination of ergoloid mesylate and Ergosta-5,7,9(11),22-tetraen-3-ol, (3.beta.,22E)- with binding affinities of -15.5 kcal/mol, and -11.3 kcal/mol respectively. Further, MD simulation and PCA analyses showed that the phytochemicals possessed significant binding efficacy with CC protein. These results point the way for more investigation into SHPE compound's potential as CC treatment.

Effect of temperature on hepatitis a virus and exploration of binding mode mechanism of phytochemicals from tinospora cordifolia: an insight into molecular docking, MM/GBSA, and molecular dynamics simulation study

The hepatitis A virus (HAV), which causes hepatitis A, is a contagious liver ailment. The infections are not specifically treated by any medications. Therefore, the development of less harmful, more effective and cost-effective antiviral agents are necessary. The present work highlighted the in-silico activity of phytocompounds from tinospora cordifolia against HAV. The binding interaction of HAV with the phytocompounds was analyzed through molecular docking. Molecular docking revealed that chasmanthin, malabarolide, menispermacide, tinosporaside, and tinosporinone compounds bind with HAV more efficiently than other compounds. Further evaluation using 100 ns molecular dynamics simulation, MM/GBSA and free energy landscape indicated that all phytocompounds studied here were found to be most promising drug candidate against hepatitis A virus. Our computational study will encourage promoting in further investigation for in vitro and in vivo clinical trials.Communicated by Ramaswamy H. Sarma.

Study of the Sensing Kinetics of G Protein-Coupled Estrogen Receptor Sensors for Common Estrogens and Estrogen Analogs

Endogenous and exogenous estrogens are widely present in food and food packaging, and high levels of natural estrogens and the misuse or illegal use of synthetic estrogens can lead to endocrine disorders and even cancer in humans. Therefore, it is consequently important to accurately evaluate the presence of food-functional ingredients or toxins with estrogen-like effects. In this study, an electrochemical sensor based on G protein-coupled estrogen receptors (GPERs) was fabricated by self-assembly, modified by double-layered gold nanoparticles, and used to measure the sensing kinetics for five GPER ligands. The interconnected allosteric constants (K_a) of the sensor for 17β-estradiol, resveratrol, G-1, G-15, and bisphenol A were 8.90 × 10^-17, 8.35 × 10^-16, 8.00 × 10^-15, 5.01 × 10^-15, and 6.65 × 10^-16 mol/L, respectively. The sensitivity of the sensor for the five ligands followed the order of 17β-estradiol > bisphenol A > resveratrol > G-15 > G-1. The receptor sensor also demonstrated higher sensor sensitivity for natural estrogens than exogenous estrogens. The results of molecular simulation docking showed that the residues Arg, Glu, His, and Asn of GPER mainly formed hydrogen bonds with -OH, C-O-C, or -NH-. In this study, simulating the intracellular receptor signaling cascade with an electrochemical signal amplification system enabled us to directly measure GPER-ligand interactions and explore the kinetics after the self-assembly of GPERs on a biosensor. This study also provides a novel platform for the accurate functional evaluation of food-functional components and toxins.