Molecular docking analysis of GC-MS analyzed bioactive compounds from the rhizome of Hedychium rubrum with four protein targets.

Hedychium rubrum, a traditional medicinal plant of Manipur belonging to the family Zingeberaceae was screened for its biological activity. The methanolic extract of its rhizome was prepared by Soxhlet extraction method and was further subjected to GC-MS to know its bioactive compounds. The in vitro antimicrobial activity assay was tested against five bacteria causing UTI. Klebseilla pneumoniae showed most sensitive followed by Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus and Enterococcus faecalis in the order. Plant extract showed higher inhibition zone than the positive control used. According to the higher quality of compounds from the GCMS results nine compounds were selected for further in silico studies using GOLD software against four protein targets. The phytoconstituents present in the methanolic extract have the ability to bind at the receptor site of all four targeted proteins. ADMET and TOPKAT studies were also carried out.

A prospective compound screening contest identified broader inhibitors for Sirtuin 1.

Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified.

The crystal structures and Hirshfeld surface analyses of four 3,5-diacetyl-2-methyl-2,3-di-hydro-1,3,4-thia-diazol-2-yl derivatives.

The title compounds, 4-(5-acetamido-3-acetyl-2-methyl-2,3-di-hydro-1,3,4-thia-diazol-2-yl)phenyl benzoate, C20H19N3O4S (I), 4-(5-acetamido-3-acetyl-2-methyl-2,3-di-hydro-1,3,4-thia-diazol-2-yl)phenyl isobutyrate 0.25-hydrate, C17H21N3O4S·0.25H2O (II), 4-(5-acetamido-3-acetyl-2-methyl-2,3-di-hydro-1,3,4-thia-diazol-2-yl)phenyl propionate, C16H19N3O4S (III) and 4-(5-acetamido-3-acetyl-2-methyl-2,3-di-hydro-1,3,4-thia-diazol-2-yl)phenyl cinnamate chloro-form hemisolvate, C22H21N3O4S·0.5CHCl3 (IV), all crystallize with two independent mol-ecules (A and B) in the asymmetric unit in the triclinic P space group. Compound II crystallizes as a quaterhydrate, while compound IV crystallizes as a chloro-form hemisolvate. In compounds I, II, III (mol-ecules A and B) and IV (mol-ecule A) the five-membered thia-diazole ring adopts an envelope conformation, with the tetra-substituted C atom as the flap. In mol-ecule B of IV this ring is flat (r.m.s. deviation 0.044 Å). The central benzene ring is in general almost normal to the mean plane of the thia-diazole ring in each mol-ecule, with dihedral angles ranging from 75.8 (1) to 85.5 (2)°. In the crystals of all four compounds, the A and B mol-ecules are linked via strong N-H⋯O hydrogen bonds and generate centrosymmetric four-membered R 4 4(28) ring motifs. There are C-H⋯O hydrogen bonds present in the crystals of all four compounds, and in I and II there are also C-H⋯π inter-actions present. The inter-molecular contacts in the crystals of all four compounds were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.

Influence of handle shape and size to reduce the hand-arm vibration discomfort.

BACKGROUND: Non-automated tool handles transmit a large magnitude of vibration to operators' hands, causing discomfort and pain. Therefore, the need for a better handle design is a matter of prime concern to overcome musculoskeletal disorders such as hand-arm vibration syndrome. OBJECTIVE: This study aimed to examine the influence of handle shapes in reducing the transmission of hand-arm vibration. METHODS: Seven different handles were designed and fabricated using 3D printing technology at the SSN College of Engineering, with consideration for the anatomical shape of the hand. The frequency-weighted Root Mean Square (RMS) values of the vibration levels transmitted were recorded at the wrist of twelve subjects, unaffected by musculoskeletal disorders. Subjective ratings of vibration and comfort perception were measured using the Borg Scale of Perceived Exertion. RESULTS: The total vibration value (ahv) of each of the six novel prototype handles (B-G) was compared to that of the reference handle denoted handle-A. The vibration reductions for handles B to G respectively were 0.542 m/s2 (14.59%), 0.481 m/s2 (12.95%), 0.351 m/s2 (9.45%), 0.270 m/s2 (7.27%), 0.407 m/s2 (10.96%) and 0.192 m/s2 (5.17%). CONCLUSIONS: A significant level of vibration reduction was achieved by the prototype handles. Qualitative feedback from the study subjects suggests that they were not aware of the levels of vibration being transmitted to the hand with each handle.

The crystal structures of 6'-(4-chloro-phen-yl)- and 6'-(4-meth-oxy-phen-yl)-6a'-nitro-6a',6b',7',9',10',12a'-hexa-hydro-2H,6'H,8'H-spiro-[ace-naphthyl-ene-1,12'-chromeno[3,4-a]indolizin]-2-one.

In the title compounds, C32H25ClN2O4 (I) and C33H28N2O5 (II), the six-membered pyran and piperidine rings adopt envelope and chair conformations, respectively. The five-membered pyrrolidine rings adopt twist conformations. Compound (II) crystallizes with two independent mol-ecules (A and B) in the asymmetric unit. In all three mol-ecules there is a C-H⋯O intra-molecular hydrogen bond present enclosing an S(7) ring motif. In (I), both oxygen atoms of the nitro group are disordered, while in (II) the meth-oxy-benzene group is disordered in mol-ecule B. The geometries were regularized by soft restraints. In the crystal of (I), mol-ecules are linked by C-H⋯O hydrogen bonds, forming chains along [010]. The chains are linked by C-H⋯Cl hydrogen bonds, forming layers parallel to (10). Within the layer there are C-H⋯π inter-actions present. In the crystal of (II), the A and B mol-ecules are linked via C-H⋯O hydrogen bonds, forming a square four-membered A-B-A-B unit. These units are linked by a number of C-H⋯π inter-actions, forming a three-dimensional supra-molecular structure.

Crystal structure of 6-(4-chloro-phen-yl)-6a-nitro-6a,6b,8,9,10,12a-hexa-hydro-6H,7H-spiro[chromeno[3,4-a]indolizine-12,11'-indeno-[1,2-b]quinoxaline].

The title compound, C35H27ClN4O3, crystallized with two independent mol-ecules (A and B) in the asymmetric unit. In both mol-ecules, the pyran and pyridine rings adopt envelope and chair conformations, respectively. The conformation of the pyrrolidine and cyclo-pentene rings differ in the two mol-ecules; twisted and flat, respectively, in mol-ecule A, but envelope and twisted, respectively, in mol-ecule B. In both mol-ecules, there is a C-H⋯N intra-molecular hydrogen bond present. In both mol-ecules, the oxygen atoms of the nitro groups are disordered as is the chlorine atom in mol-ecule B. In the crystal, the B mol-ecules are linked by C-H⋯O hydrogen bonds, forming -B-B-B- chains along [010], and by C-H⋯π inter-actions. The A and B mol-ecules are also linked by a number of C-H⋯π inter-actions, resulting in the formation a supra-molecular three-dimensional structure. In mol-ecule A, the nitro group oxygen atoms are disordered over two positions with refined occupancy ratios of the nitro group oxygen atoms O3A and O4A in 0.59 (2):0.41 (2) while in molecule B one of the nitro O atoms is disordered over two positions with a refined occupancy ratio of 0.686 (13):0.314 (13) and the chlorine atoms is disordered over two positions with a refined occupancy ratio of 0.72 (3):0.28 (3).

Flavonoids modulate multidrug resistance through wnt signaling in P-glycoprotein overexpressing cell lines.

BACKGROUND: Wnt signaling has been linked with P-glycoprotein (P-gp) overexpression and which was mainly mediated by ß-catenin nuclear translocation. Flavonoids have already been reported as modulators of the Wnt/ß-catenin pathway and hence they may serve as promising agents in the reversal of P-gp mediated cancer multi drug resistance (MDR). METHODS: In this study, we screened selected flavonoids against Wnt/ß-catenin signaling molecules. The binding interaction of flavonoids (theaflavin, quercetin, rutin, epicatechin 3 gallate and tamarixetin) with GSK 3ß was determined by molecular docking. Flavonoids on P-gp expression and the components of Wnt signaling in drug-resistant KBCHR8-5 cells were analyzed by western blotting and qRT-PCR. The MDR reversal potential of these selected flavonoids against P-gp mediated drug resistance was analyzed by cytotoxicity assay in KBCHR8-5 and MCF7/ADR cell lines. The chemosensitizing potential of flavonoids was further analyzed by observing cell cycle arrest in KBCHR8-5 cells. RESULTS: In this study, we observed that the components of Wnt/ß-catenin pathway such as Wnt and GSK 3ß were activated in multidrug resistant KBCHR8-5 cell lines. All the flavonoids selected in this study significantly decreased the expression of Wnt and GSK 3ß in KBCHR8-5 cells and subsequently modulates P-gp overexpression in this drug-resistant cell line. Further, we observed that these flavonoids considerably decreased the doxorubicin resistance in KBCHR8-5 and MCF7/ADR cell lines. The MDR reversal potential of flavonoids were found to be in the order of theaflavin > quercetin > rutin > epicatechin 3 gallate > tamarixetin. Moreover, we observed that flavonoids pretreatment significantly induced the doxorubicin-mediated arrest at the phase of G2/M. Further, the combinations of doxorubicin with flavonoids significantly modulate the expression of drug response genes in KBCHR8-5 cells. CONCLUSION: The present findings illustrate that the studied flavonoids significantly enhances doxorubicin-mediated cell death through modulating P-gp expression pattern by targeting Wnt/ß-catenin signaling in drug-resistant KBCHR8-5 cells.

Structural data of DNA binding and molecular docking studies of dihydropyrimidinone transition metal complexes.

A series of some novel copper complexes derived from Biginelli condensation of DHPHS. The ligand and its transition metal complexes show more antimicrobial activities which was substantiated by molecular docking studies. Transition metal complexes four possess antioxidant properties supported by the DNA-binding, cleavage, and viscosity measurement (Prasad et al., 2011) [1]. The in Silicon DNA binding reveals copper complex is bound to be Minor groove and other manganese, cobalt, nickel complexes are bound to the Major groove portion of DNA through hydrogen bonds and hence copper (II), manganese (II), cobalt (II), nickel (II) complexes are called Minor groove and Major groove binder respectively. The DNA cleavage studies of metal complexes presented more protruding activity in the attendance of H2O2 associated to that in the absence of H2O2. In continuance of our ongoing research on DNA binding and cleavage happenings of transition metal complexes, in this paper we obtainable the synthesis, characterization and DNA cleavage activities.

Structural insights and binding of a natural ligand, succinic acid with serine and cysteine proteases.

In the age of growing infectious diseases, there is a great demand for new inhibitors which can exhibit minimum side effects. Owing to the importance of proteases in life cycle and invasion, they have been projected as attractive targets for structure based drug designing against microbes including viruses. Here we report the inhibitory activity of a well known natural compound succinic acid against both serine and cysteine proteases. The ligand is found co-crystallized with Bovine pancreatic trypsin in one of our crystallization trials and the diffraction data up to1.9 Å reveal its interactions with the catalytic triad residues Histidine 57 and Serine 195. Binding of the ligand with these proteases have been validated using caseinolysis inhibition. With trypsin, ITC analysis showed tight binding of the ligand, resulting in change in Gibb's free energy (ΔG) by -20.31 kJ/mol. To understand the existence of succinic acid at the active site, molecular docking was performed and it revealed binding of it with trypsin and papain at corresponding active sites. This dual inhibitory activity of natural ligand, succinic acid can be accounted for the recent reports on anti-viral property of plant extracts where dicarboxilic fatty acids are normally abundant.

Molecular docking and molecular dynamics simulations of fumarate hydratase and its mutant H235N complexed with pyromellitic acid and citrate.

Fumarase catalyzes the reversible, stereospecific hydration/dehydration of fumarate to L-malate during the Kreb's cycle. In the crystal structure of the tetrameric fumarase, it was found that some of the active site residues S145, T147, N188 G364 and H235 had water-mediated hydrogen bonding interactions with pyromellitic acid and citrate which help to the protonation state for the conversion of fumarate to malate. When His 235 is mutated with Asn (H235N), water-mediated interactions were lost due to the shifting of active site water molecule by 0.7 Å away. Molecular dynamics (MD) simulations were also carried out by NAMD and analyzed using Assisted Model Building with Energy Refinement (AMBER) program to better understand the conformational stability and other aspects during the binding of pyromellitic acid and citrate with native and mutant FH. The role of hydrogen bonds and hydrophobic interactions was also analyzed. The present study confirms that the H235N mutation has a major effect on the catalytic activity of fumarase which is evident from the biochemical studies.

Purification and characterization of an anti-hemorrhagic protein from Naja naja (Indian cobra) venom.

Snake venom Kunitz-type proteins are well known to inhibit serine proteases but a few studies have also shown matrix metalloproteases (MMPs) inhibition. In view of the fact that MMPs and snake venom metalloproteases (SVMPs) have similar catalytic site, inhibition of SVMP activity by Kunitz-type proteins remains to be studied. Recent proteomic studies of Naja naja (N. naja) venom revealed the abundance of Kunitz-type proteins. In this regard, present study aimed at purification of a protease inhibitor from N. naja venom that inhibits the toxicity of SVMPs rich Echis carinatus (E. carinatus) venom. N. naja venom effectively inhibited E. carinatus venom-induced hemorrhage. Purification of the active principle responsible for anti-hemorrhagic effect was achieved by fractionation of N. naja venom in three successive chromatographic steps. SDS-PAGE revealed that purified anti-hemorrhagic protein (NNAh) has an apparent molecular mass of ∼44 kDa and single peak in RP-HPLC demonstrated its homogeneity. NNAh also inhibited myonecrosis induced by E. carinatus venom and reduced activity of creatine kinase in NNAh treated animal sera substantiated the anti-myonecrotic effect. Hemorrhage and myonecrosis inhibitory effects of NNAh were further supported by inhibition of E. carinatus venom-mediated gelatinolysis and collagenolysis. NNAh falls into the category of Kunitz-type serine protease inhibitor as determined by peptide mass fingerprinting and shown to be a strong inhibitor of chymotrypsin. Collectively our data signify that NNAh is a Kunitz-type chymotrypsin inhibitor which also inhibited metalloprotease activities of E. carinatus venom. In future, complete sequence of NNAh and peptide region(s) responsible for inhibition will assist to deduce the mechanism of action.

An iterative compound screening contest method for identifying target protein inhibitors using the tyrosine-protein kinase Yes.

We propose a new iterative screening contest method to identify target protein inhibitors. After conducting a compound screening contest in 2014, we report results acquired from a contest held in 2015 in this study. Our aims were to identify target enzyme inhibitors and to benchmark a variety of computer-aided drug discovery methods under identical experimental conditions. In both contests, we employed the tyrosine-protein kinase Yes as an example target protein. Participating groups virtually screened possible inhibitors from a library containing 2.4 million compounds. Compounds were ranked based on functional scores obtained using their respective methods, and the top 181 compounds from each group were selected. Our results from the 2015 contest show an improved hit rate when compared to results from the 2014 contest. In addition, we have successfully identified a statistically-warranted method for identifying target inhibitors. Quantitative analysis of the most successful method gave additional insights into important characteristics of the method used.

Possible role of Epoxyeicosatrienoic acid in prevention of oxidative stress mediated neuroinflammation in Parkinson disorders.

Parkinson's disease (PD) is a multifactorial neurodegenerative disease involving oxidative stress, neuroinflammation and apoptosis. Epoxyeicosatrienoic acids (EETs) are arachidonic acid metabolites and they play a role in cytoprotection by modulating various cell signaling pathways. This cytoprotective role of EETs are well established in cerebral stroke, cardiac failure, and hypertension, and it is due to their ability to attenuate oxidative stress, endoplasmic reticulum stress, inflammation, caspase activation and apoptosis. The actions of EETs in brain closely parallel the effects which is observed in the peripheral tissues. Since many of these effects could potentially contribute to neuroprotection, EETs are, therefore, one of the potential therapeutic candidates in PD. Therefore, by increasing the half life of endogenous EETs in vivo via inhibition of sEH, its metabolizing enzyme can, therefore, constitutes an important therapeutic strategy in PD.

PDBparam: Online Resource for Computing Structural Parameters of Proteins.

Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. In this work, we have developed a web-based tool, PDBparam, for computing more than 50 structure-based features for any given protein structure. These features are classified into four major categories: (i) interresidue interactions, which include short-, medium-, and long-range interactions, contact order, long-range order, total contact distance, contact number, and multiple contact index, (ii) secondary structure propensities such as α-helical propensity, ß-sheet propensity, and propensity of amino acids to exist at various positions of α-helix and amino acid compositions in high B-value regions, (iii) physicochemical properties containing ionic interactions, hydrogen bond interactions, hydrophobic interactions, disulfide interactions, aromatic interactions, surrounding hydrophobicity, and buriedness, and (iv) identification of binding site residues in protein-protein, protein-nucleic acid, and protein-ligand complexes. The server can be freely accessed at http://www.iitm.ac.in/bioinfo/pdbparam/. We suggest the use of PDBparam as an effective tool for analyzing protein structures.

Screening dietary flavonoids for the reversal of P-glycoprotein-mediated multidrug resistance in cancer.

P-Glycoprotein (P-gp) serves as a therapeutic target for the development of inhibitors to overcome multidrug resistance in cancer cells. Although various screening procedures have been practiced so far to develop first three generations of P-gp inhibitors, their toxicity and drug interaction profiles are still a matter of concern. To address the above important problem of developing safe and effective P-gp inhibitors, we have made systematic computational and experimental studies on the interaction of natural phytochemicals with human P-gp. Molecular docking and QSAR studies were carried out for 40 dietary phytochemicals in the drug-binding site of the transmembrane domains (TMDs) of P-gp. Dietary flavonoids exhibit better interactions with homology modeled human P-gp. Based on the computational analysis, selected flavonoids were tested for their inhibitory potential against P-gp transport function in drug resistant cell lines using calcein-AM and rhodamine 123 efflux assays. It has been found that quercetin and rutin were the highly desirable flavonoids for the inhibition of P-gp transport function and they significantly reduced resistance in cytotoxicity assays to paclitaxel in P-gp overexpressing MDR cell lines. Hence, quercetin and rutin may be considered as potential chemosensitizing agents to overcome multidrug resistance in cancer.

CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation.

Accurate distinction between peptide sequences that can form amyloid-fibrils or amorphous ß-aggregates, identification of potential aggregation prone regions in proteins, and prediction of change in aggregation rate of a protein upon mutation(s) are critical to research on protein misfolding diseases, such as Alzheimer's and Parkinson's, as well as biotechnological production of protein based therapeutics. We have developed a Curated Protein Aggregation Database (CPAD), which has collected results from experimental studies performed by scientific community aimed at understanding protein/peptide aggregation. CPAD contains more than 2300 experimentally observed aggregation rates upon mutations in known amyloidogenic proteins. Each entry includes numerical values for the following parameters: change in rate of aggregation as measured by fluorescence intensity or turbidity, name and source of the protein, Uniprot and Protein Data Bank codes, single point as well as multiple mutations, and literature citation. The data in CPAD has been supplemented with five different types of additional information: (i) Amyloid fibril forming hexa-peptides, (ii) Amorphous ß-aggregating hexa-peptides, (iii) Amyloid fibril forming peptides of different lengths, (iv) Amyloid fibril forming hexa-peptides whose crystal structures are available in the Protein Data Bank (PDB) and (v) Experimentally validated aggregation prone regions found in amyloidogenic proteins. Furthermore, CPAD is linked to other related databases and resources, such as Uniprot, Protein Data Bank, PUBMED, GAP, TANGO, WALTZ etc. We have set up a web interface with different search and display options so that users have the ability to get the data in multiple ways. CPAD is freely available at http://www.iitm.ac.in/bioinfo/CPAD/. The potential applications of CPAD have also been discussed.

Autoimmune Responses to Soluble Aggregates of Amyloidogenic Proteins Involved in Neurodegenerative Diseases: Overlapping Aggregation Prone and Autoimmunogenic regions.

Why do patients suffering from neurodegenerative diseases generate autoantibodies that selectively bind soluble aggregates of amyloidogenic proteins? Presently, molecular basis of interactions between the soluble aggregates and human immune system is unknown. By analyzing sequences of experimentally validated T-cell autoimmune epitopes, aggregating peptides, amyloidogenic proteins and randomly generated peptides, here we report overlapping regions that likely drive aggregation as well as generate autoantibodies against the aggregates. Sequence features, that make short peptides susceptible to aggregation, increase their incidence in human T-cell autoimmune epitopes by 4-6 times. Many epitopes are predicted to be significantly aggregation prone (aggregation propensities ≥10%) and the ones containing experimentally validated aggregating regions are enriched in hydrophobicity by 10-20%. Aggregate morphologies also influence Human Leukocyte Antigen (HLA)--types recognized by the aggregating regions containing epitopes. Most (88%) epitopes that contain amyloid fibril forming regions bind HLA-DR, while majority (63%) of those containing amorphous ß-aggregating regions bind HLA-DQ. More than two-thirds (70%) of human amyloidogenic proteins contain overlapping regions that are simultaneously aggregation prone and auto-immunogenic. Such regions help clear soluble aggregates by generating selective autoantibodies against them. This can be harnessed for early diagnosis of proteinopathies and for drug/vaccine design against them.