Antiviral compound screening, peptide designing, and protein network construction of influenza a virus (strain a/Puerto Rico/8/1934 H1N1).

Plant-based antiviral therapy is the current need for holistic health care management, which can be achieved through screening of phytochemicals and designing of antiviral peptides. There exist certain host's factors which are directly involved for rapid viral replication causing worldwide pandemic. A total of 177 phytochemicals from Ocimum sanctum (L.), Tinospora cordifolia (Thunb.) Miers, Cinnamomum camphora (L.) J. Presl., Allium sativum (L.), Curcuma longa (L.), and Aloe vera (L.) Burm. f. were evaluated for their affinity to all viral proteins of H1N1. Applying drug filters and keeping the threshold of such filters relative to the standards, 82 compounds were found suitable for further analysis. Consensus scoring system was used for screening top ligands from 82 compounds, which screened the top 12 compounds. Highly conserved regions (>80%) which were hydrophilic, flexible, antigenic, and also charged were screened out as potent antiviral peptides. The viral proteins were taken as the targets for the modeled peptides for protein-protein docking. Further, host-pathogen interacting network was constructed to unveil host factors involved in viral replication, from which unique protein clusters representing their involvement in viral reproduction were selected through mapping with pathway databases. Twelve compounds and five peptides were found to be highly effective against all the proteins of H1N1. Based on the uniqueness, 13 clusters of proteins were obtained which are engaged in cellular process, namely, viral reproduction, fructose-6-phosphate metabolism, nitrogen compound metabolism, biosynthesis, cellular process, oligodendrocyte development, localization, multiorganism process, primary metabolism, response to unfolded protein, metabolism, and response to protein and catabolism.

Bacteria in the oral cavity of individuals consuming intoxicating substances.

Food habits and oral hygiene are critical attributes for physiochemical environment of the oral cavity. Consumption of intoxicating substances such as betel nut ('Tamul'), alcohol, smoking and chewing tobacco may strongly influence the oral ecosystem including commensal microbes. Therefore, a comparative assessment of microbes in the oral cavity between individuals consuming intoxicating substances and non-consumers may indicate the influence of these substances. Oral swabs were collected from consumers of intoxicating substances and non- consumers of Assam, India, microbes were isolated by culturing on Nutrient agar and identified by phylogenetic analysis of their 16S rRNA gene sequences. The risks of consumption of intoxicating substance on occurrence of microbes and health conditions were estimated using binary logistic regression. Mostly pathogens and opportunistic pathogens were found in the oral cavity of consumers and oral cancer patients which included Pseudomonas aeruginosa, Serratia marcescens, Rhodococcus antrifimi, Paenibacillus dendritiformis, Bacillus cereus, Staphylococcus carnosus, Klebsiella michiganensis and Pseudomonas cedrina. Enterobacter hormaechei was found in the oral cavity of cancer patients but not in other cases. Pseudomonas sp. were found to be widely distributed. The risk of occurrence of these organisms were found in between 0.01 and 2.963 odds and health conditions between 0.088 and 10.148 odds on exposure to different intoxicating substances. When exposed to microbes, the risk of varying health conditions ranged between 0.108 and 2.306 odds. Chewing tobacco showed a higher risk for oral cancer (10.148 odds). Prolonged exposure to intoxicating substances conduce a favorable environment for the pathogens and opportunistic pathogens to colonize in the oral cavity of individuals consuming intoxicating substances.

Established and In-trial GPCR Families in Clinical Trials: A Review for Target Selection.

The largest family of drug targets in clinical trials constitute of GPCRs (G-protein coupled receptors) which accounts for about 34% of FDA (Food and Drug Administration) approved drugs acting on 108 unique GPCRs. Factors such as readily identifiable conserved motif in structures, 127 orphan GPCRs despite various de-orphaning techniques, directed functional antibodies for validation as drug targets, etc. has widened their therapeutic windows. The availability of 44 crystal structures of unique receptors, unexplored non-olfactory GPCRs (encoded by 50% of the human genome) and 205 ligand receptor complexes now present a strong foundation for structure-based drug discovery and design. The growing impact of polypharmacology for complex diseases like schizophrenia, cancer etc. warrants the need for novel targets and considering the undiscriminating and selectivity of GPCRs, they can fulfill this purpose. Again, natural genetic variations within the human genome sometimes delude the therapeutic expectations of some drugs, resulting in medication response differences and ADRs (adverse drug reactions). Around ~30 billion US dollars are dumped annually for poor accounting of ADRs in the US alone. To curb such undesirable reactions, the knowledge of established and currently in clinical trials GPCRs families can offer huge understanding towards the drug designing prospects including "off-target" effects reducing economical resource and time. The druggability of GPCR protein families and critical roles played by them in complex diseases are explained. Class A, class B1, class C and class F are generally established family and GPCRs in phase I (19%), phase II(29%), phase III(52%) studies are also reviewed. From the phase I studies, frizzled receptors accounted for the highest in trial targets, neuropeptides in phase II and melanocortin in phase III studies. Also, the bioapplications for nanoparticles along with future prospects for both nanomedicine and GPCR drug industry are discussed. Further, the use of computational techniques and methods employed for different target validations are also reviewed along with their future potential for the GPCR based drug discovery.

Phylogenetic affiliation and antimicrobial effects of endophytic actinobacteria associated with medicinal plants: prevalence of polyketide synthase type II in antimicrobial strains.

The most diverse and versatile endophytic actinobacteria are relatively unexplored potential sources of bioactive metabolites useful for different medical, agricultural, and other commercial applications. Their diversity in symbiotic association with traditionally utilized medicinal plants of northeast India is scantly available. The present investigation assessed the genetic diversity of endophytic actinobacteria (n = 120) distributed around the root, stem, and leaf tissues of six selected medicinal plants (Emblica officinalis, Terminalia chebula, T. arjuna, Murraya koenigii, Rauwolfia serpentina, and Azadirachta indica) from three different protected areas of evergreen forest-the Gibbon Wildlife Sanctuary (GWS), the Kaziranga National Park (KNP), and the North East Ecological Park (NEEP) of Assam, India. The samples were collected in two seasons (summer and winter). The overall phylogenetic analysis showed significant genetic diversity with 18 distinct genera belonging to 12 families. Overall, the occurrence of Streptomyces genus was predominant across all three sampling sites (76.66%), in both the sampling season (summer and winter). Shannon's and Simpson's diversity estimates showed their presence at A. indica (1.496, 0.778), R. serpentina (1.470, 0.858), and E. officinalis (0.975, 0.353). Among the site sampled, GWS had the most diverse community of actinobacteria (Shannon = 0.86 and Simpson = 0.557). The isolates were antagonistically more active against the investigated plant pathogenic bacteria than fungal pathogens. Further analysis revealed the prevalence of polyketide synthase genes (PKS) type II (84%) and PKS type I (16%) in the genome of the antimicrobial isolates. The overall findings confirmed the presence of biosynthetically active diverse actinobacterial members in the selected medicinal plants which offer potential opportunities towards the exploration of biologically active compounds.

Volatile Inhibitors of Phosphatidylinositol-3-Kinase (PI3K) Pathway: Anticancer Potential of Aroma Compounds of Plant Essential Oils.

BACKGROUND: Cancer is a grave health problem for the world as the global cancer burden rises to 14 million new cases with 8.2 million deaths every year which is expected to rise by 70% in the next 2 decades as reported by the WHO.These steady rises in death demand for rapid developments in anti-cancer agents. Essential oils, being natural and multi-component complex systems have recently attracted a lot of attention in this search for novel anti-cancer agents. MATERIALS AND METHODS: The pharmaceutical attributes of essential oil components, specifically focusing on their affinity towards COX, 5-LOX, AKT, MDM2, PDK1 and mTOR which defines the phosphatidylinositol-3- kinase (PI3K) pathway, were assessed. 123 compounds present in essential oils of different plants were analyzed for their drug like attributes which were then allowed to dock with PI3K dependent receptors crucial for the development of cancer malignancies. Among them, 21 compounds were filtered possessing high druglikeness with favourable metabolism offered by major cytochromeP450 isoforms. Finally, the best docked compounds with highest binding affinities were employed for building a ligand based pharmacophore. Being inhibitors of P-glycoproteins, these molecules also exhibited good absorption profiles and noncarcinogenic properties. Further from these 21, six compounds were evaluated against A549 lung cancer cells. RESULTS: The pharmacophoric feature obtained can be applied for both designing and screening moieties for active inhibitors of the phosphatidylinositol-3-kinase pathway specifically from essential oil compounds and these final 21 compounds can be further promoted to studies for anti-cancer drug development. Among these, six compounds exhibited promising inhibitory results against A549 lung cancer cells. Furthermore, immunoblotting assay confirmed the efficacy of the compounds for inhibiting mTOR and AKT enzymes which are bandmasters for downstream signaling of thePI3K pathway. CONCLUSION: Methyl nonanoate, (R)-citronellol, cis-carveol (L-carveol), 3-methyl-Cyclohexanone, 4-carene and thujopsene were finally screened for PI3K targeted anti-cancer therapies which may find direct application as inhalers or sprays against lung cancer as these compounds are highly volatile.

Modelling and Characterization of Glial Fibrillary Acidic Protein.

Glial Fibrillary Acidic Protein (GFAP) is an intermediate-filament (IF) protein that maintains the astrocytes of the Central Nervous System in Human. This is differentially expressed during serological studies in inflamed condition such as Rheumatoid Arthritis (RA). Therefore, it is of interest to glean molecular insight using a model of GFAP (49.88 kDa) due to its crystallographic nonavailability. The present study has been taken into consideration to construct computational protein model using Modeller 9.11. The structural relevance of the protein was verified using Gromacs 4.5 followed by validation through PROCHECK, Verify 3D, WHAT-IF, ERRAT and PROVE for reliability. The constructed three dimensional (3D) model of GFAP protein had been scrutinized to reveal the associated functions by identifying ligand binding sites and active sites. Molecular level interaction study revealed five possible surface cavities as active sites. The model finds application in further computational analysis towards drug discovery in order to minimize the effect of inflammation.

Insights from the predicted interactions of plant derived compounds to the gluco-corticoid receptor as an alternative to dexa-methasone.

Dexamethasone (DEX) an anti-inflamatory 9-fluoro-glucocorticoid, activates the cytosolic glucocorticoid receptor (GR) binding to its Ligand Binding Domain (LBD). The GR-ligand complex then translocates to the nucleus and binds to the Glucocorticoid Response Element (GRE) resulting up-regulation of target gene expression of anti-inflamatory proteins. DEX is one of the most effective ligand for GR activation but comply to side effects. Therefore, alternative for DEX - plant metabolites of Calotropis sp and Swertia chirata were screened using docking appraoch. These plants compounds were selected because; parts of these plants are widely used againsts inflamation, allergy, asthma etc. Three metabolites of Swertia chirata namely Gentianine (GENT), Xanthone (XANT) and Swerchirin (SWER) are found to be occupying the same binding pocket in the LBD of the GR (PDB ID 1M2Z). The binding affinity as reflected by binding energies of GENT-1M2Z, XANT-1M2Z and SWER-1M2Z are -5.6, -6.7 and -6.7, and all the output parameter of the respective compounds positively correlates with that of DEX-1M2Z with r = 0.9, 0.6 and 0.6 respectively indicating similar GR activation function. Visualization analysis of the models clearly indicates that GENT and SWER may be GR activators. Rest of the compounds mostly docked onto the surface of the receptor molecule.

Insights from the docking analysis of biologically active compounds from plant Litsea Genus as potential COX-2 inhibitors.

Litsea spp of Laural family are traditionally used as herbal medicine for treating inflammation including gastroenterologia, oedema and rheumatic arthritis. Therefore, it is of interest to investigate and understand the molecular principles for such actions. Here, we have illustrated the binding of thirteen Litsea derived biologically active compounds against the inflammation associated target COX (cyclo-oxygenase) -2 enzymes. We compared the binding information of these compounds with a selected number of already known COX-2 inhibitors. The comparison reflected that some of these compounds such as linderol, catechin, 6'-hydroxy-2',3',4' - trimethoxy-chalcone and litseaone have better or equivalent binding features compared to already known inhibitory compounds namely celecoxib, acetylsalicylic acid, rofecoxib. Therefore, all these small compounds reported from plant Litsea spp were found to possess potential medicinal values with anti-inflammatory properties.