Ingestion of microplastics and its potential for causing structural alterations and oxidative stress in Indian green mussel Perna viridis- A multiple biomarker approach.

The present study has investigated the distribution of microplastics in sediment and its impact on histological, ultrastructural, and oxidative stress mechanisms in Perna viridis (P. viridis) from Kasimedu, Chennai, India. The results confirmed that fibers were the predominant type of microplastics observed, followed by spheres, flakes, sheets, and fragments. The observed microplastics were confirmed as polyester, polypropylene, polyethylene, cellophane, and rayon using µ-FT-IR. Microplastic particles entangled in gills caused abrasion of ciliated structure and hemocyte infiltration in the hemolymph vessels. The digestive gland showed a shrunken nucleus, dark inclusions, and damage in the nucleoid core structure. Enlarged vacuoles and the presence of clusters of vesicles presumably represented the transformed golgi cisternae. Further, the results confirmed that oxidative stress markers were significantly high in gills and digestive diverticula of P. viridis. Overall, the results indicated that microplastics induced different toxic physiological and structural alterations in gills and digestive diverticula of P. viridis. These findings highlighted the necessity to focus on exposure studies to understand the absolute magnitude of the problem due to microplastic pollution in the urban estuarine ecosystems of Chennai, Tamil Nadu, India.

Delineating binding potential, stability of Sulforaphane-N-acetyl-cysteine in the active site of histone deacetylase 2 and testing its cytotoxicity against distinct cancer lines through stringent molecular dynamics, DFT and cell-based assays.

Histone deacetylase 2 (HDAC2), an isozyme of Class I HDACs has potent imputations in actuating neurodegenerative signaling. Currently, there are sizeable therapeutic disquiets with the use of synthetic histone deacetylase inhibitors in disease management. This strongly suggests the unfulfilled medical necessity of plant substitutes for therapeutic intervention. Sulforaphane-N-acetyl-cysteine (SFN-N-acetylcysteine or SFN-NAC), a sulforaphane metabolite has shown significantly worthier activity against HDACs under in vitro conditions. However, the atomistic studies of SFN-NAC against HDAC2 are currently lacking. Thus, the present study employed a hybrid strategy including extra-precision (XP) grid-based flexible molecular docking, molecular mechanics generalized born surface area (MM-GBSA), e-Pharmacophores method, and molecular dynamics simulation for exploring the binding strengh, mode of interaction, e-Pharmacophoric features, and stability of SFN-NAC towards HDAC2. Further, the globally acknowledged density functional theory (DFT) study was performed on SFN-NAC and entinostat individually in complex state with HDAC2. Apart from this, these inhibitors were tested against three distinct cancer cell models and one transformed cell line for cytotoxic activity. Moreover, double mutant of HDAC2 was generated and the binding orientation and interaction of SFN-NAC was scrutinized in this state. On the whole, this study unbosomed and explained the comparatively higher binding affinity of entinostat for HDAC2 and its wide spectrum cytotoxicity than SFN-NAC.

Morphological characterization and biocontrol effects of Vibrio vulnificus phages against Vibriosis in the shrimp aquaculture environment.

The re-emerging field of phage therapy is the potential biocontrol agents for the transfer of virulence factor and to kill their bacterial hosts. In this study, the lytic Vibrio vulnificus phages were studied to provide a better understanding of phage-host interactions and development of phage therapy. Four new V. vulnificus phages were detected from shrimp aquaculture system, named VV1, VV2, VV3 and VV4. All lytic V. vulnificus phages are the Tectiviruses of the family Tectiviridae with typical double layered elongated icosahedral head and tailless morphology. Lytic V. vulnificus phages which infect other Vibrio isolates were further characterized by long term storage, enzymes treatment, organic solvents treatment, detergents treatment, pH stability, temperature stability, agar bioassay method and one-step growth experiment. The effects of chloroform, acetone, ethyl alcohol, methyl alcohol, ribonuclease (RNase), trypsin, protease, Triton-X100 treatments were not affected the growth of VV1, VV2, VV3 and VV4 phages. These phages (VV1-VV4) were inactivated completely with temperature (over 60 °C), pH (<3 or >12), lysozyme and sodium dodecyl sulfate (SDS) treatment. One-step growth experiments indicated that the latent period was at 3 h and burst size was at 37 °C. Agar bioassay method indicated that the percentage of inhibition was 75% (VV1) and 70% (VV2, VV3 & VV4), respectively. SDS-PAGE analysis of all V. vulnificus phages had similar protein patterns with molecular weight masses of 260, 249, 204, 148, 63, 59, 22 and 15 kDa. Hence, it could be concluded that V. vulnificus phage had a broad lytic spectrum and potential biocontrol of luminous Vibriosis in the shrimp aquaculture system.

Efficacy of potential phage cocktails against Vibrio harveyi and closely related Vibrio species isolated from shrimp aquaculture environment in the south east coast of India.

A diverse set of novel phages infecting the marine pathogenic Vibrio harveyi was isolated from shrimp aquaculture environments in the south east coast of India. Based on initial screening, three phages with a broad host range revealed that the growth inhibition of phage is relatively specific to V. harveyi. They were also able to infect V. alginolyticus and V. parahemolyticus that belonged to the Harveyi clade species from shrimp pond and sea coast environment samples. However, the impact of these phages on their host bacterium are well understood; a one-step growth curve experiment and transmission electron microscope (TEM) revealed three phages grouped under the Myoviridae (VHM1 and VHM2); Siphoviridae (VHS1) family. These phages were further molecular characterized with respect to phage genomic DNA isolates. The randomly amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP) digestion with HindIII, and major structural proteins were distinguished by sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) clearly indicated that all the phage isolates were different, even when they came from the same source, giving an insight into the diversity of phages. Evaluation of microcosm studies of Penaeus monodon larvae infected with V. harveyi (105 CFU mL-1) showed that larvae survival after 96 h in the presence of phage treatment at 109 PFU mL-1 was enhanced when compared with the control. The resolution in over survival highly recommended that this study provides the phage-based therapy which could be an innovative and eco-friendly solution against Vibrio disease in shrimp aquaculture and in the natural environment.

Molecular Docking, Molecular Dynamics Simulations, Computational Screening to Design Quorum Sensing Inhibitors Targeting LuxP of Vibrio harveyi and Its Biological Evaluation.

Quorum sensing (QS) plays an important role in the biofilm formation, production of virulence factors and stress responses in Vibrio harveyi. Therefore, interrupting QS is a possible approach to modulate bacterial behavior. In the present study, three docking protocols, such as Rigid Receptor Docking (RRD), Induced Fit Docking (IFD), and Quantum Polarized Ligand Docking (QPLD) were used to elucidate the binding mode of boronic acid derivatives into the binding pocket of LuxP protein in V. harveyi. Among the three docking protocols, IFD accurately predicted the correct binding mode of the studied inhibitors. Molecular dynamics (MD) simulations of the protein-ligand complexes indicates that the inter-molecular hydrogen bonds formed between the protein and ligand complex remains stable during the simulation time. Pharmacophore and shape-based virtual screening were performed to find selective and potent compounds from ChemBridge database. Five hit compounds were selected and subjected to IFD and MD simulations to validate the binding mode. In addition, enrichment calculation was performed to discriminate and separate active compounds from the inactive compounds. Based on the computational studies, the potent Bicyclo [2.2.1] hept-5-ene-2,3-dicarboxylic acid-2,6-dimethylpyridine 1-oxide (ChemBridge_5144368) was selected for in vitro assays. The compound exhibited dose dependent inhibition in bioluminescence and also inhibits biofilm formation in V. harveyi to the level of 64.25 %. The result from the study suggests that ChemBridge_5144368 could serve as an anti-quorum sensing molecule for V. harveyi.

Pharmacophore modeling, comprehensive 3D-QSAR, and binding mode analysis of TGR5 agonists.

Takeda G-protein-coupled receptor 5 (TGR5) is emerging as an important and promising target for the development of anti-diabetic drugs. Pharmacophore modeling and atom-based 3D-QSAR studies were carried out on a new series of 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides as highly potent agonists of TGR5. The generated best six featured pharmacophore model AAHHRR consists of two hydrogen bond acceptors (A): two hydrophobic groups (H) and two aromatic rings (R). The constructed 3D-QSAR model acquired excellent correlation coefficient value (R2 = 0.9018), exhibited good predictive power (Q2 = 0.8494) and high Fisher ratio (F = 61.2). The pharmacophore model was validated through Guner-Henry (GH) scoring method. The GH value of 0.5743 indicated that the AAHHRR model was statistically valuable and reliable in the identification of TGR5 agonists. Furthermore, the combined approach of molecular docking and binding free energy calculations were carried out for the 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides to explore the binding mode and interaction pattern. The generated contour maps revealed the important structural insights for the activity of the compounds. The results obtained from this study could be helpful in the development of novel and more potent agonists of TGR5.

Discovery of potent inhibitors targeting Vibrio harveyi LuxR through shape and e-pharmacophore based virtual screening and its biological evaluation.

Quorum sensing is widely recognized as an efficient mechanism in the regulation and production of several virulence factors, biofilm formation and stress responses. For this reason, quorum sensing circuit is emerging as a novel drug target for the development of anti-infective. Recently, cinnamaldehyde derivatives have been found to interfere with master quorum sensing transcriptional regulator and thereby decreasing the DNA binding ability of LuxR. However, the exact mode of cinnamaldehyde binding with LuxR and receptor interaction still remains inconclusive. In the current study, combined method of molecular docking and molecular dynamics simulations were performed to investigate the binding mode, dynamic and energy aspects of cinnamaldehyde derivatives into the binding site of LuxR. Based on the experimental and computational evidences, LuxR-3,4-dichloro-cinnamaldehyde complex was chosen for the development of e-pharmacophore model. Further, shape and e-pharmacophore based virtual screening were performed against ChemBridge database to find potent and suitable ligands for LuxR. By comparing the results of shape and e-pharmacophore based virtual screening; best 9 hit molecules were selected for further studies including ADMET prediction, molecular dynamics simulations and Prime MM-GBSA calculations. From the 9 hit molecules, the top most compound 3-(2,4-dichlorophenyl)-1-(1H-pyrrol-2-yl)-2-propen-1-one (ChemBridge-7364106) was selected for in vitro assays using Vibrio harveyi. The result revealed that ChemBridge-7364106 significantly reduced the bioluminescence production in a dose dependent manner. In addition, ChemBridge-7364106 showed a significant inhibition in biofilm formation and motility in V. harveyi. The results from the study suggest that ChemBridge-7364106 could serve as an anti-quorum sensing molecule for V. harveyi.

Binding mode exploration of LuxR-thiazolidinedione analogues, e-pharmacophore-based virtual screening in the designing of LuxR inhibitors and its biological evaluation.

Master quorum sensing (QS) regulator LuxR of Vibrio harveyi is a unique member of the TetR protein superfamily. Recent studies have demonstrated the contribution of thiazolidinedione analogues in blocking QS by decreasing the DNA-binding ability of LuxR. However, the precise mechanism of thiazolidinedione analogues binding to LuxR is still unclear. In the present study, molecular docking combined with molecular dynamics (MD) simulations was performed to understand the mechanism of ligand binding to the protein. The binding pattern of thiazolidinedione analogues showed strong hydrogen bonding interactions with the amine group (NH) of polar amino acid residue Asn133 and carbonyl (C=O) interaction with negatively charged amino acid residue Gln137 in the binding site of LuxR. The stability of the protein-ligand complexes was confirmed by running 50 ns of MD simulations. Further, the four-featured pharmacophore hypothesis (AHHD) consists of one acceptor (A), two hydrophobic regions (HH) and one donor (D) group was used to screen compounds from ChemBridge database. The identified hit molecules were shown to have excellent pharmacokinetic properties under the acceptable range. Based on the computational studies, ChemBridge_5343641 was selected for in vitro assays. The 1-(4-chlorophenoxy)-3-[(4,6-dimethyl-2-pyrimidinyl)thio]-2-propanol (ChemBridge_5343641) showed significant reduction in bioluminescence in a dose-dependent manner. In addition, ChemBridge_5343641 inhibits biofilm formation and motility in V. harveyi. The result from the study suggests that ChemBridge_5343641 could serve as an anti-QS molecule.

Characterization of Vibrio parahaemolyticus and its specific phage from shrimp pond in Palk Strait, South East coast of India.

Phage therapy is an alternative and eco-friendly biocontrol agent to prevent and control multidrug resistant bacteria in the aquatic system. The aim of this study is to isolate and characterize the Vibrio parahaemolyticus and its potential lytic phage from Penaeus monodon growing-out by rearing in shrimp ponds in Palk Strait, South East coast of India. The conventional phenotypic characteristics and molecular identification was confirmed using 16S rRNA sequence and to determine the antibiotic resistant profiles. The V. parahaemolyticus phage was effective against V. parahaemolyticus through one-step growth experiments, phage survival was determined by long-term storage at various temperatures and pH. Further, transmission electron microscope (TEM) revealed that the lytic phage belongs to the Myoviridae family. The isolated lytic phage (VVP1) was more specific against N1A V. parahaemolyticus and was able to infect N7A V. parahaemolyticus, N3B and N13B Vibrio alginolyticus strains. Evaluation of microcosm studies with P. monodon larvae infected with V. parahaemolyticus showed the survival of larvae in the presence of phage treatment at 2.3 × 1010 PFU/mL-1 was enhanced when compared with the control. This study provides the application of phage as a useful strategy to prevent and eliminate or reduce shrimp pathogenic V. parahaemolyticus in the aquaculture system.

Characterization of potential lytic bacteriophage against Vibrio alginolyticus and its therapeutic implications on biofilm dispersal.

Vibrio alginolyticus is a leading cause of vibriosis, presenting opportunistic infections to humans associated with raw seafood contamination. At present, phage therapy that acts as an alternative sanitizing agent is explored for targeting V. alginolyticus. The study outcome revealed that the phage VP01 with its extreme lytic effect showed a high potential impact on the growth of V. alginolyticus as well as biofilm formation. Electron microscopy revealed the phage resemblance to Myoviridae, based on its morphology. Further study clarified that the phage VP01 possesses a broad host spectrum and amazing phage sensitivity at different pH, high thermal stability, and high burst size of 415 PFU/cell. In addition, the investigation of phage co-culturing against this pathogen resulted in a significant growth reduction even at less MOIs 0.1 and 1. These results suggest that the phage could be a promising candidate for the control of V. alginolyticus infections.

Molecular characterization of antibiotic resistant Vibrio harveyi isolated from shrimp aquaculture environment in the south east coast of India.

Vibrio harveyi is a strategic human pathogen that occurs naturally in marine and estuarine environments. The pathogen is believed to cause acute septicemia, gastroenteritis, severe necrotizing soft-tissue infection, and high rate of lethality through ingestion of V. harveyi contaminated seafood. In this study, we isolated and characterized V. harveyi from water suspended sediment samples of black tiger shrimp ponds and from the sea coasts, in the east coast of the Bay of Bengal, India. Initial isolations of putative V. harveyi isolates were grown on thiosulfate-citrate-bill salts-sucrose agar (TCBS) plates for 36 h. Gram-negative and oxidase-positive colonies alone were selected and subsequently identified by 12 different conventional biochemical tests. The species specificity was confirmed by 16S rRNA, hemolysin and toxRvh genes were used through PCR targeted primers. Furthermore, genomic fingerprinting was carried out using randomly amplified polymorphic DNA fingerprinting, which showed that all the five V. harveyi were genetically distinct. From a total of 256 samples, a total of five strains of V. harveyi were isolated, of which three were from various shrimp ponds and two were from the coastal area. These five isolates were subjected to profiling against 15 antibiotics and the perusal results emphasized the V. harveyi resistance to ciprofloxacin, penicillin, rifampicin, and vancomycin compared to other tested antibiotics. The present findings were helpful in understanding the multiple antibiotics resistance of V. harveyi, which indicates the urgent need for targeted alternative biocontrol strategies to enhance the prospects of commercially viable shrimp cultivation.

Pharmacophore modeling and structure-based virtual screening to identify potent inhibitors targeting LuxP of Vibrio harveyi.

The main aim of the study is to identify molecules that can disrupt quorum sensing (QS) system of Vibrio harveyi and therefore perhaps the production of toxins. Recently, a novel class of dioxazaborocane derivatives has been found to block AI-2 QS by targeting LuxPQ, but the mechanism of protein inhibition is still unclear. In order to investigate the possible binding modes, all the derivatives were docked into the binding site of LuxP using induced fit docking (IFD). The computed binding affinity is in good agreement with the experimental data. Resultant protein-ligand complexes were simulated using Desmond module and the result revealed better binding of ligands in the binding site of LuxP. Both pharmacophore- and structure-based virtual screening was performed to identify novel hits against LuxP. A filtering protocol, including lipinski filters, number of rotatable bonds and three levels of docking precisions were used for the selection of hits with specific properties. The virtual screening results were then combined and analyzed, which retrieved six hits with significant Glide score, binding affinity toward LuxP. The pharmacokinetic properties of the retrieved hits are in the acceptable range. Enrichment calculation was performed to validate the final hits, to discriminate the active compounds from the inactive compounds. The identified hits could serve as a base for further drug development against LuxP of Vibrio harveyi.

Structural insights on identification of potential lead compounds targeting WbpP in Vibrio vulnificus through structure-based approaches.

WbpP encoding UDP-GlcNAC C4 epimerase is responsible for the activation of virulence factor in marine pathogen Vibrio vulnificus (V. vulnificus) and it is linked to many aquatic diseases, thus making it a potential therapeutic target. There are few reported compounds that include several natural products and synthetic compounds targeting Vibrio sp, but specific inhibitor targeting WbpP are unavailable. Here, we performed structure-based virtual screening using chemical libraries such as Binding, TOSLab and Maybridge to identify small molecule inhibitors of WbpP with better drug-like properties. Deficient structural information forced to model the structure and the stable protein structure was obtained through 30 ns of MD simulations. Druggability regions are focused for new lead compounds and our screening protocol provides fast docking of entire small molecule library with screening criteria of ADME/Lipinski filter/Docking followed by re-docking of top hits using a method that incorporates both ligand and protein flexibility. Docking conformations of lead molecules interface displays strong H-bond interactions with the key residues Gly101, Ser102, Val195, Tyr165, Arg298, Val209, Ser142, Arg233 and Gln200. Subsequently, the top-ranking compounds were prioritized using the molecular dynamics simulation-based conformation and stability studies. Our study suggests that the proposed compounds may aid as a starting point for the rational design of novel therapeutic agents.

An anthraquinone derivative from Luffa acutangula induces apoptosis in human lung cancer cell line NCI-H460 through p53-dependent pathway.

The current study was designed to evaluate the in vitro antiproliferative activity of 1,8-dihydroxy-4-methylanthracene-9,10-dione (DHMA) isolated from the Luffa acutangula against human non-small cell lung cancer cell line (NCI-H460). Induction of apoptosis and reactive oxygen species (ROS) generation was determined through fluorescence microscopic technique. Quantitative real-time PCR and western blotting analysis was carried out to detect the expression of pro-apoptotic (p53, p21, caspase-3, Bax, GADD45A, and ATM) and anti-apoptotic (NF-κB) proteins in NCI-H460 cell line. In silico studies also performed to predict the binding mechanism of DHMA with MDM2-p53 protein. The DHMA inhibited the cell viability of NCI-H460 cells in a dose-dependent manner with an IC(50) of about 50 µg/ml. It significantly reduced cell viability correlated with induction of apoptosis, which was associated with ROS generation. The apoptotic cell death was further confirmed through dual staining and DNA fragmentation assay. DHMA significantly increased the expression of anti-apoptotic protein such as p53, p21, Bax, and caspase-3 but downregulated the expression of NF-κB in NCI-H460 cell line. In silico studies demonstrate that DHMA formed hydrogen bond interaction with key residues Trp26, Phe55 and Lys24 by which it disrupt the binding of p53 with MDM2 receptor. These findings suggested that DHMA induces apoptosis in NCI-H460 via a p53-dependent pathway. This the first study on cytotoxic and apoptosis inducing activity of DHMA from L. acutangula against NCI-H460 cell line. Therefore, DHMA has therapeutic potential for lung cancer treatment.

In vitro, fluorescence-quenching and computational studies on the interaction between lipoxygenase and 5-hydroxy-3',4',7-trimethoxyflavone from Lippia nodiflora L.

Lippia nodiflora L. is extensively used in traditional medicine for several medicinal purposes, including their use in inflammatory disorders. In this study, the folk use of L. nodiflora was validated using the isolated natural compound, 5-hydroxy-3',4',7-trimethoxyflavone (HTMF) by in vitro, fluorescence spectroscopic and molecular modeling studies with lipoxygenase (LOX), because LOX plays an essential role in inflammatory responses. In this perspective, the methanol extract and HTMF are shown to demonstrate prominent inhibitory activity against soybean lipoxygenase, with an IC50 value of 21.12 and 23.97 µg/ml, respectively. The data obtained from the spectroscopic method revealed that the quenching of intrinsic fluorescence of LOX is produced as a result of the complex formation of LOX-HTMF. The binding mode analysis of HTMF within the LOX enzyme suggested that hydrogen bond formation, hydrophobic interaction and π-π stacking could account for the binding of HTMF. Molecular dynamics results indicated the interaction of HTMF with LOX and the stability of ligand-enzyme complex was maintained throughout the simulation. The computational results are reliable with experimental facts and provided a good representation for understanding the binding mode of HTMF inside the active site of lipoxygenase enzyme.

Identification of potential dual agonists of FXR and TGR5 using e-pharmacophore based virtual screening.

Farnesoid X receptor and Takeda G-protein-coupled receptor-5 are well known bile acid receptors and act as promising targets for the drug development and treatment of diabetes. Agonists of both the bile acid receptors increase insulin sensitivity and control glucose, lipids and bile acid homeostasis. The current study deals with the identification of novel dual agonists using ligand and structure-based virtual screening. Initially, an experimentally proven well-known dual agonist of FXR and TGR5, namely INT-767, was docked into the binding sites of FXR and TGR5 to determine the protein residues important for ligand binding. The docked complexes FXRINT-767 and TGR5INT-767 were used to generate e-pharmacophore hypotheses. Ligand-based virtual screening was carried out using the hypothetical e-pharmacophore model against the ChemBridge database. Further, structure-based virtual screening was performed with screened hits to find potential agonists of FXR and TGR5. A total of four best agonists were identified based on their affinity and mode of interactions with the receptors. The binding mode of these compounds with both receptors was analyzed in detail. Furthermore, molecular dynamics, ADME toxicity prediction, density functional theory and binding free energy calculations were carried out to rank the compounds. Based on the above analyses, the most potent compound, ChemBridge_9149693, was selected for further in vitro studies. The results of in vitro assays suggested that ChemBridge_9149693 is a potent and promising drug for the treatment of type II diabetes. Thus, the compound could be used for further drug design and development of dual agonists of FXR and TGR5.

Exploration of potential EGFR inhibitors: a combination of pharmacophore-based virtual screening, atom-based 3D-QSAR and molecular docking analysis.

Epidermal growth factor receptor (EGFR) protein tyrosine kinases are over expressed in several human cancers and considered as a promising target for developing novel anticancer drugs. In this study, the ligand-based pharmacophore mapping and atom-based 3D-QSAR approach was carried out on a series of 40 novel pyrrolo[3, 2-d]pyrimidine derivatives acting as EGFR inhibitors. The best pharmacophore hypothesis AAADRR.295 was selected and an atom-based 3D-QSAR model was generated by applying partial least-squares algorithm. The developed model was validated and used as a 3D query in sequential virtual screening study to filter five chemical databases. The obtained compounds were further filtered according to Lipinski rule of five and fitness score. Subsequently, a multistep molecular docking study was employed on the retrieved hits and finally, 12 compounds were prioritized as potential leads against EGFR, which exhibited high docking scores, correlated binding mode to experimentally proven compounds and constructive drug-like properties. The results of this study provide detailed structural insights and emphasize the important binding features of these compounds, which may assists in the design and development of novel EGFR inhibitors.

Bioassay-guided isolation and identification of bioactive compound from aerial parts of Luffa acutangula against lung cancer cell line NCI-H460.

Luffa acutangula (Cucurbitaceae) is widely used as a traditional medicine in India and was reported to possess various pharmacological activities including its anti-proliferative effects. In this study, the bioactive compound of ethanolic extract of L. acutangula (LA) was isolated using bioassay-guided approach. Five major fractions were collected and evaluated for their anti-proliferative activity against non-small cell lung cancer cells (NCI-H460). Among the test fractions, the fraction LA/FII effectively decreased the growth of cancer cells with IC50 values of 10 µg/ml concentration. Furthermore, it significantly increased intracellular reactive oxygen species and decreased the mitochondrial membrane potential. The apoptogenic activity of fraction LA/FII was confirmed by cell shrinkage, membrane blebbing and formation of apoptotic bodies. A single bioactive compound was isolated from the active faction, LA/FII and subsequently identified as 1,8 dihydroxy-4-methylanthracene 9,10-dione (compound 1) by comparing its spectral data [Ultraviolet (UV), Infrared (IR), Nuclear magnetic resonance (NMR) and Electrospray Ionization-Mass Spectroscopy (ESI-MS)] with literature values. This is the first report on the isolation of compound 1 from this plant.

Pharmacophore modeling, 3D-QSAR and molecular docking studies of benzimidazole derivatives as potential FXR agonists.

Farnesoid X receptor (FXR) is a potential therapeutic target for the treatment of diabetes mellitus. Atom-based three-dimensional quantitative structure activity relationship (3D-QSAR) models were developed for a series of 48 benzimidazole-based agonists of FXR. A total of five pharmacophore hypotheses were generated based on the survival score to build QSAR models. HHHRR was considered as a best model that consisted of three hydrophobic features (H) and two aromatic rings (R). The best hypothesis, HHHRR yielded a 3D-QSAR model with good statistical value (R(2)) of 0.8974 for a training set of 39 compounds and also showed good predictive power with correlation coefficient (Q(2)) of 0.7559 for a test set of nine compounds. Furthermore, molecular docking simulation was performed to understand the binding affinity of 48 benzimidazole-based compounds against the active site of human FXR protein. Docking results revealed that both the most active and least active compounds showed similar binding mode to the experimentally observed binding mode of co-crystallized ligand. The generated 3D contour maps revealed the structure activity relationship of the compounds. Substitution effects at different positions of benzimidazole derivatives would lead to the discovery of new agonists against human FXR protein.

Epitope-based immunoinformatics and molecular docking studies of nucleocapsid protein and ovarian tumor domain of crimean-congo hemorrhagic Fever virus.

Crimean-Congo hemorrhagic fever virus (CCHFV), the fatal human pathogen is transmitted to humans by tick bite, or exposure to infected blood or tissues of infected livestock. The CCHFV genome consists of three RNA segments namely, S, M, and L. The unusual large viral L protein has an ovarian tumor (OTU) protease domain located in the N terminus. It is likely that the protein may be autoproteolytically cleaved to generate the active virus L polymerase with additional functions. Identification of the epitope regions of the virus is important for the diagnosis, phylogeny studies, and drug discovery. Early diagnosis and treatment of CCHF infection is critical to the survival of patients and the control of the disease. In this study, we undertook different in silico approaches using molecular docking and immunoinformatics tools to predict epitopes which can be helpful for vaccine designing. Small molecule ligands against OTU domain and protein-protein interaction between a viral and a host protein have been studied using docking tools.