Exploring binding mode assessment of novel kaempferol, resveratrol, and quercetin derivatives with PPAR-α as potent drug candidates against cancer.

Peroxisome proliferator-activated receptors (PPAR)-α, a ligand-activated transcription factor stands out to be a valuable protein target against cancer. Given that ligand binding is the crucial process for the activation of PPAR-α, fibrate class of synthetic compounds serves as potent agonist for the receptor. However, their serious side effects limit the long-term application in cancer. This emphasizes the dire need to identify new candidates that would exert desired activation by abrogating the adverse effects caused by synthetic agonists. Natural dietary products serve as an important source of drug discovery. Hence, the present study encompasses the investigation of the role of natural plant phenolic compounds: kaempferol, resveratrol, and quercetin and their 8708 derivatives by the means of computational pipeline comprising molecular docking and molecular dynamic (MD) simulation techniques. Docking calculations shortlisted potential candidates, namely 6-cinnamylchrysin (6-CC), resveratrol potassium-4-sulfate (RPS) and 6-[2-(3,4-Dihydroxyphenyl)-5-hydroxy-4-oxochromen-7-yl]oxyhexyl nitrate (DHOON), and derivatives of kaempferol, resveratrol, and quercetin, respectively. 6-CC, RPS, and DHOON manifested better affinities of - 32.83 kcal/mol (Ala333, Lys358, His440), - 27.22 kcal/mol (Tyr314, Met355), and - 30.18 kcal/mol (Ser280, Tyr314, Ala333), respectively, and were found to act as good stimulants for PPAR-α. Among these three compounds, 6-CC caused relatively least deviations and fluctuations analyzed through MD simulation which judiciously held responsible to attain most favorable interaction with PPAR-α. Followed by the binding free energy (ΔG) calculations using MM-GBSA confirmed the key role of 6-CC toward PPAR-α. The compound 6-CC also achieved high drug-likeness and pharmacokinetic properties. Thus, these findings stipulate new drug leads for PPAR-α receptor which abets a way to develop new anti-cancer drugs.

Dual inhibition of cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) by resveratrol derivatives in cancer therapy: in silico approach.

In a number of human cancers, both cycloxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX) are up-regulated and co-expressed, promoting cancer cell proliferation and angiogenesis. Resveratrol (3,4',5-trihydroxy-trans-stilbene) is a natural polyphenolic phytoalexin found in a variety of plants that influences various signal-transduction pathways which control apoptosis, cell growth and cell division, metastasis, angiogenesis and inflammation, and has an impact on cancer stages ranging from initiation to progression. In this work, molecular docking and molecular dynamics simulation method are employed to design resveratrol derivatives for COX-2 and 5-LOX enzymes. By attaching several functional groups on four different places of the resveratrol scaffold, the R group enumeration approach was employed to build four libraries of resveratrol derivatives. Thus, R group enumeration is done to focus on the enhancement of potency of compounds and other chemical characteristics like solubility. Drug-like filters such as REOS 1, 2, 3 and PAINS were applied to the libraries, generating a total of 5557 compounds. Drug-like filters such as REOS and PAINS-1, 2 and 3 were applied to the libraries, generating a total of 5557 compounds. All of these compounds were docked with both enzymes using the Glide SP and XP docking methods. Enrichment calculations were performed using 40 compounds from XP docking along with resveratrol, and 1000 decoy compounds from the DUD-E database to validate the docking protocol. The stability of the complexes was further studied using molecular dynamics simulation, radius of gyration, MM/GBSA, H bond monitoring and electrostatic potential surface (EPS). ADMET properties of compounds were studied using SwissADME and pkCSM server.Communicated by Ramaswamy H. Sarma.

Comprehensive molecular docking and dynamic simulations for drug repurposing of clinical drugs against multiple cancer kinase targets.

Drug repurposing is a method to identify novel therapeutic agents from the existing drugs and clinical compounds. In the present comprehensive work, molecular docking, virtual screening and dynamics simulations were carried out for ten cancer types viz breast, colon, central nervous system, leukaemia, melanoma, ovarian, prostate, renal and lung (non-small and small cell) against validated eighteen kinase targets. The study aims to understand the action of chemotherapy drugs mechanism through binding interactions against selected targets via comparative docking simulations with the state-art molecular modelling suits such as MOE, Cresset-Flare, AutoDock Vina, GOLD and GLIDE. Chemotherapeutic drugs (n = 112) were shortlisted from standard drug databases with appropriate chemoinformatic filters. Based on docking studies it was revealed that leucovorin, nilotinib, ellence, thalomid and carfilzomib drugs possessed potential against other cancer targets. A library was built to enumerate novel molecules based on the scaffold and functional groups extracted from known drugs and clinical compounds. Twenty novel molecules were prioritised further based on drug-like attributes. These were cross docked against 1MQ4 Aurora-A Protein Kinase for prostate cancer and 4UYA Mitogen-activated protein kinase for renal cancer. All docking programs yielded similar results but interestingly AutoDock Vina yielded the lowest RMSD with the native ligand. To further validate the final docking results at atomistic level, molecular dynamics simulations were performed to ascertain the stability of the protein-ligand complex. The study enables repurposing of drugs and lead identification by employing a host of structure and ligand based virtual screening tools and techniques.Communicated by Ramaswamy H. Sarma.

Transferrin binding protein-B from Neisseria meningitidis C as a novel carrier protein in glycoconjugate preparation: an in silico approach.

The linking of polysaccharide in glycoconjugate vaccine with carrier protein is an imperative step to develop a strong memory response. The excessive use of similar carrier protein known to result in bystander immunity warrants an urgent need for new carrier protein. The preparation of the glycoconjugate vaccine using cyanylation chemistry is to link the active cyanate ester site of polysaccharide with the carrier protein. In the present study, transferrin binding protein-B (Tbp-B) has been explored as a new carrier protein to develop in silico pneumococcal polysaccharide serotype-5 (PnPs-5) conjugate vaccine. The homology model of Tbp-B was constructed using the Prime module and stereochemically validated using ProSA, PDBsum and ProQ. The selected model revealed a Z-score of -5.6 within the X-ray region in ProSA analysis, LGscore: 9.776, and MaxSub: 0.8 in protein quality predictor suggesting its preferred use. Loop modeling and active site analysis followed by in silico PnPs-5 activation with cyanalyting agent CDAP was docked with Tbp-B using Glide module. The complex stability of cyanate esters with Tbp-B, analyzed by molecular dynamics (MD) simulation, revealed an average RMSD of 2.49 Å for its binding to the receptor. The RMSF values of cyanate ester-1, -2, and -3 were observed to be 1.06, 1.39 and 0.79 Å, respectively. The higher RMSF of 1.39 Å of cyanate ester-2 was further found unstable which corroborates its non-binding to the protein and also incurring conformational changes to a carrier protein. Molecular simulations revealed that cyanate ester-1 and cyanate ester-3 formed stable conjugates with carrier protein Tbp-B. Communicated by Ramaswamy H. Sarma.

A clinical study of benign tumours of nose and paranasal sinuses.

In this prospective study, comprising of 30 cases, various benign tumours, both common and rare are compiled. The cases were selected in the OPD of Kempegowda institute of medical sciences, one of the tertiary referral centres in Bangalore. The sample consists of patients in the age group 9 months to 60 years. The study also compares sex differences,symptomatology and the relative incidence of various rumours. The commonest site was nasal cavity, followed by paranasal sinuses and external nose. They occur commonly in second and third decades with predominance in males. Epithelial tumours were less common when compared to non epithelial tumours. All masses should be subjected to histopathological examination for proper management All cases should be followed up for as long as two years for better assessment treatment and response.

Rat brain thioltransferase: regional distribution, immunological characterization, and localization by fluorescent in situ hybridization.

Thioltransferase (TTase) is a member of the family of thiol-disulfide oxidoreductases that are involved in the maintenance of sulfhydryl homeostasis in cells by catalyzing thiol-disulfide interchange reactions. One of the major consequences of oxidative stress in brain is the formation of protein-glutathione mixed disulfides (through oxidation of protein thiols), which can be reversed by TTase during the recovery of brain from oxidative stress. We therefore examined the presence of TTase in brain regions from rat. In the rat, TTase activity in the whole brain was comparable with the corresponding activity in liver, but significantly higher in hippocampus. The enzyme activity was significantly lower in striatum and cerebellum compared with activity in whole brain. Rat brain TTase shared immunological similarity with the human red blood cell enzyme, but not with the pig liver enzyme. The constitutive expression of the mRNA to TTase was demonstrable by northern blotting. Localization of the TTase mRNA in rat brain by fluorescent in situ hybridization showed the presence of high amounts of mRNA in the olfactory bulb, cortex, and hippocampus and its predominant localization in the neurons. TTase mRNA was also present in Purkinje cells in the cerebellum, in giant reticular neurons in the midbrain, and in the striatal and thalamic neurons. This study demonstrates the constitutive presence of a functional TTase system in brain and delineates the regional and cellular localization of the enzyme in rat brain.

Action of the herbicide butachlor on cholinesterases in the freshwater snail Pila globosa (Swainson).

Butachlor action on acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activates in central nervous tissue of the snail Pila globosa was assayed following the method of ELLMAN et al1, in vitro by adding butachlor directly (10-100 mu moles), to tissue homogenates and in in vivo by exposing the snails to sub-lethal concentration (26.6 ppm) and taking out the tissue for experimentation at different intervals (3, 6, 12, 24 and 48 h) of exposure. The enzyme activities decreased in a dose-dependent manner in vitro, and up to 12-24 h in vivo after which they showed recovery towards the control. The inhibition of cholinesterases by butachlor in vitro indicates a direct action of the herbicide on these enzymes. Presumably butachlor exercises its neurotoxic effects through cholinergic impairment in a way similar to that of organophosphates and carbamates.

Butachlor impact on protein, free amino acid and glutamine contents, and on activity levels of aminotransferases, glutamate dehydrogenase and glutamine synthetase in the fresh water snail, Pila globosa (Swainson).

Biochemical changes followed in the freshwater snail Pila globosa (Swainson) during exposure to sublethal concentrations of the herbicide butachlor (26.6 ppm) in the ambient medium, at 3,6,12,24 and 48 h intervals, were marked by a significant decrease in total and soluble proteins, and an increase in free amino acids in foot and hepatopancreas up to 12 h before gradually recovering. Aminotransferase activities and glutamine content decreased during the early periods of exposure, while glutamate dehydrogenase activity increased. After an initial elevation, glutamate synthetase activity decreased at later intervals. Maximum effect of butachlor on the enzymes was seen after 12 h exposure. The extent of increase or decrease in different parameters examined varied between the two tissues studied. These changes are discussed in relation to the toxic stress of butachlor.

Changes in cholinesterase system in different brain areas during the development of behavioral tolerance to monocrotophos toxicity in male albino rats.

During the development of behavioral tolerance to the organophosphate monocrotophos, the activities of AChE and BuChE and the content of ACh were affected in different brain areas of male albino rats. The inhibition of AChE and BuChE activities and the elevation of ACh content were progressive till 7 days and were followed by a recovery trend towards normalcy. The changes correlated with the appearance and disappearance of signs and symptoms of toxicity, which were mainly cholinergic. The results suggest the possibility of de novo synthesis of cholinesterases resulting in the development of behavioral tolerance, as was evident by the recovery trend. The shift of toxicity from greater AChE inhibition during initial periods to greater BuChE inhibition during later periods indicates the possible involvement of pseudocholinesterases in the development of tolerance and in the reduction of toxicity. The brain areas were differentially affected. Cerebral cortex was more affected initially but it was the striatum that was affected more during later dosings. The results show that behavioral tolerance to monocrotophos toxicity develops despite changes in AChE and BuChE activities and ACh content.

Effect of monocrotophos on mono amine oxidase activity in albino rats.

Monocrotophos inhibited monoamine oxidase (MAO) activity both in vitro and in vivo in liver, kidney and brain areas of albino rats. In vitro effect was more pronounced than the in vivo effect. During in vivo daily treatment with sublethal doses of Monocrotophos, the MAO activity was significantly inhibited after 1h to 7 days of treatments. Later recovery of inhibition was noticed which might be attributed to the enhanced absorption of Monocrotophos to protein and fat bodies or enhanced metabolic dispositional mechanisms. Brain areas exhibit varied responses to Monocrotophos toxicity.