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.

Green Synthesis of Copper Oxide Nanoparticles Using Coix lacryma jobi Leaves Extract and Screening of its Potential Anticancer Activities

Background: Copper oxide nanoparticles(CuO NPs) have been powerful evidence in several in vitro studies such as cytotoxicity and antimicrobial compared with other metal oxide. Here, we have synthesized green CuO NPs using Coix lacryma jobi leaves extracts. Place and Duration of Study: Department of Chemistry  Manipur University, Manipur, India and Regional Institute of Medical Sciences, Imphal, India between February 2019 to March 2021. Methodology: Green CuO NPs nanoparticles were synthesized from Copper chloride dihydrate (CuCl2.2H2O) using Coix lacryma jobi leaves extract, and the synthesized green CuO NPs were characterized using Field Emission Scanning Electron Microscopy (FESEM) - Energy Dispersive Spectroscopy, IR Spectroscopy, UV-Visible Spectroscopy, Powder X-Ray diffraction Spectroscopy and HR-TEM where FESEM-EDS determined the purity of CuO NPs. Results: No other impurities present were observed in EDS, and the PXRD spectra show the crystallite size of CuO NPs with respect to the (002) plane is found to be 25.2 nm, and the presence of CuO NPs at adsorption spectrum with a distinct peak at 282 nm was determined by  UV-Visible spectroscopy and the homogenous morphology and crystalline nature of the CuO NPs were determined from TEM micrograph and SAED pattern. In applications, the substantial anticancer activity of green CuO NPs (synthesized using Coix lacryma jobi leaves extract) was proved on human cervical and lung cancer cell lines with IC50 values of 31.88 μg/ml and 15.61 μg/ml, respectively.

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 crystal structures of four 3,5-diacetyl-2-methyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl derivatives, viz. 4-phenyl benzoate, 4-phenyl isobutyrate, 4-phenyl propionate and 4-phenyl cinnamate, are described and the inter­molecular contacts in the crystals are analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.

The title compounds, 4-(5-acetamido-3-acetyl-2-methyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl)phenyl benzoate, C₂₀H₁₉N₃O₄S (I), 4-(5-acetamido-3-acetyl-2-methyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl)phenyl isobutyrate 0.25-hydrate, C₁₇H₂₁N₃O₄S·0.25H₂O (II), 4-(5-acetamido-3-acetyl-2-methyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl)phenyl propionate, C₁₆H₁₉N₃O₄S (III) and 4-(5-acetamido-3-acetyl-2-methyl-2,3-di­hydro-1,3,4-thia­diazol-2-yl)phenyl cinnamate chloro­form hemisolvate, C₂₂H₂₁N₃O₄S·0.5CHCl₃ (IV), all crystallize with two independent mol­ecules (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 chloro­form hemisolvate. In compounds I, II, III (mol­ecules A and B) and IV (mol­ecule A) the five-membered thia­diazole ring adopts an envelope conformation, with the tetra­substituted C atom as the flap. In mol­ecule 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 thia­diazole ring in each mol­ecule, with dihedral angles ranging from 75.8 (1) to 85.5 (2)°. In the crystals of all four compounds, the A and B mol­ecules are linked via strong N—H⋯O hydrogen bonds and generate centrosymmetric four-membered R⁴₄(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 inter­actions present. The inter­molecular contacts in the crystals of all four compounds were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.

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).

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

The conformations of the title compounds, (I) and (II), are very similar. The pyran rings adopt envelope conformations, the piperidine rings have chair conformations and the pyrrolidine rings adopt twist conformations. Intra- and inter­molecular C—H⋯O hydrogen bonds occur. Compound (II) crystallizes with two independent mol­ecules in the asymmetric unit which are linked by C—H⋯O hydrogen bonds.

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 mol­ecules (A and B) in the asymmetric unit. In all three mol­ecules there is a C—H⋯O intra­molecular hydrogen bond present enclosing an S(7) ring motif. In (I), both oxygen atoms of the nitro group are disordered, while in (II) the meth­oxy­benzene group is disordered in mol­ecule B. The geometries were regularized by soft restraints. In the crystal of (I), mol­ecules 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 inter­actions present. In the crystal of (II), the A and B mol­ecules 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 inter­actions, forming a three-dimensional supra­molecular structure.

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 β-catenin nuclear translocation. Flavonoids have already been reported as modulators of the Wnt/β-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/β-catenin signaling molecules. The binding interaction of flavonoids (theaflavin, quercetin, rutin, epicatechin 3 gallate and tamarixetin) with GSK 3β was determined by molecular docking. Flavonoids on P-gp expression and the components of Wnt signaling in drug-resistant KBCH^R8-5 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 KBCH^R8-5 and MCF7/ADR cell lines. The chemosensitizing potential of flavonoids was further analyzed by observing cell cycle arrest in KBCH^R8-5 cells.

RESULTS

In this study, we observed that the components of Wnt/β-catenin pathway such as Wnt and GSK 3β were activated in multidrug resistant KBCH^R8-5 cell lines. All the flavonoids selected in this study significantly decreased the expression of Wnt and GSK 3β in KBCH^R8-5 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 KBCH^R8-5 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 KBCH^R8-5 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/β-catenin signaling in drug-resistant KBCH^R8-5 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 H₂O_2. 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.

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.

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.

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.

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, β-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.

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.

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 β-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.

A new organic NLO material isonicotinamidium picrate (ISPA): crystal structure, structural modeling and its physico-chemical properties

A new organic nonlinear optical material isonicotinamidium picrate, with excellent nonlinear optical activity and thermal stability has been reported.

Theoretical, photophysical and biological investigations of an organic charge transfer compound 2-aminobenzimidazolium-2-oxyisoindolate-1,3-dione-2-hydroxyisoindoline-1,3-dione

The synthesized charge transfer compound exhibits excellent non-linear optical and biological properties.

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target

A search of broader range of chemical space is important for drug discovery. Different methods of computer-aided drug discovery (CADD) are known to propose compounds in different chemical spaces as hit molecules for the same target protein. This study aimed at using multiple CADD methods through open innovation to achieve a level of hit molecule diversity that is not achievable with any particular single method. We held a compound proposal contest, in which multiple research groups participated and predicted inhibitors of tyrosine-protein kinase Yes. This showed whether collective knowledge based on individual approaches helped to obtain hit compounds from a broad range of chemical space and whether the contest-based approach was effective.

Studies on the growth and characterization of a non linear optical crystal: 3 Hydroxy Pyridinium Tartrate Mono Hydrate (3HPTMH)

Single crystals of 3 Hydroxy Pyridinium Tartrate Mono Hydrate (3HPTMH) was synthesised and successfully grown in mixed solvent of ethanol and water by slow evaporation technique at room temperature. 3HPTMH belongs to the orthorhombic crystal system with space group P212121. The lattice parameters of 3HPTMH are a=7.4597(2)Å, b=8.7012(3)Å, c=17.8786(5)Å, V=1160.47(6)Å(3), obtained by single crystal X ray diffraction studies. Hyperpolarizability and HOMO-LUMO analysis were performed for grown crystal using DFT calculations using Gaussian 03 software. Functional groups were identified by FT-IR studies. The lower cut-off wavelength of the 3HPTMH has been identified by UV-Vis study. The thermal behavior has been studied by thermal gravimetric analysis and differential thermal analysis. The powder second harmonic generation efficiency of 3HPTMH was compared with KDP.

Synthesis, characterization, computational calculation and biological studies of some 2,6-diaryl-1-(prop-2-yn-1-yl)piperidin-4-one oxime derivatives

A new series of 2,6-diaryl-1-(prop-2-yn-1-yl)piperidin-4-one oximes (17-24) were designed and synthesized from 2,6-diarylpiperidin-4-one oximes (9-16) with propargyl bromide. Unambiguous structural elucidation has been carried out by investigating IR, NMR ((1)H, (13)C, (1)H-(1)H COSY and HSQC), mass spectral techniques and theoretical (DFT) calculations. Further, crystal structure of compound 17 was evaluated by single crystal X-ray diffraction analysis. Single crystal X-ray structural analysis of compound 17 evidenced that the configuration about CN double bond is syn to C-5 carbon (E-form). The existence of chair conformation was further confirmed by theoretical DFT calculation. All the synthesized compounds were screened for in vitro antimicrobial activity against a panel of selected bacterial and fungal strains using Ciprofloxacin and Ketoconazole as standards. The minimum inhibition concentration (MIC) results revealed that most of the 2,6-diaryl-1-(prop-2-yn-1-yl)piperidin-4-one oximes (17, 19, 20 and 23) exhibited better activity against the selected bacterial and fungal strains.

A bluish-green emitting organic compound methyl 3-[(E)-(2-hydroxy-1-naphthyl)methylidene]carbazate: spectroscopic, thermal, fluorescence, antimicrobial and molecular docking studies

The present paper describes the physicochemical properties and biological activities of a Schiff base compound which was grown by the slow evaporation solution growth technique.

Crystal structure of bis[4-(dimethylamino)pyridinium] bis(2-nitrobenzoate) trihydrate

The title salt, 2C7H11N2+·2C7H4NO4−·3H2O, crystallized with two anions and two cations in the asymmetric unit, together with three water molecules. Both 4-dimethylaminopyridinium cations are protonated at their pyridine N atoms with the plane of the N(CH3)2hetero atoms inclined to the pyridine ring by 4.5 (2) and 1.4 (2)°. In the 2-nitrobenzoate anions, the carboxyl and nitro groups are inclined to their respective benzene rings by 77.1 (3) and 20.0 (3)°, and 75.8 (2) and 20.9 (3)°. In the crystal, the anions are linkedviaO—H...O hydrogen bonds involving the water molecules, forming chains along [100]. The cations are linked to these chains by N—H...O hydrogen bonds. The chains are linkedviaC—H...O hydrogen bonds and C—H...π and π–π interactions [inter-centroid distances range from 3.617 (1) to 3.851 (1) Å], forming a three-dimensional structure.

(2E)-2-Benzyl-idene-9-phenyl-3,4-di-hydro-acridin-1(2H)-one

In the title compound, C₂₆H₁₉NO, the plane of the aromatic heterocycle makes a dihedral angle of 75.22 (4)° with that of the attached phenyl ring. In the crystal, mol­ecules are connected by C—H⋯O inter­actions, generating R₂²(12) dimers. These dimers are further connected by C—H⋯π inter­actions, linking the mol­ecules into chains running along the a-axis direction.

(E)-3-Isopropyl-1-methyl-2,6-di-phenyl-piperidin-4-one O-nicotinoyl oxime

In the title compound, C₂₇H₂₉N₃O₂, the piperidine ring exists in a chair conformation with an equatorial orientation of the phenyl and methyl substituents. The C—C=N bond angles are significantly different [119.1 (2) and 127.2 (2)°]. The phenyl rings are inclined to one another by 44.90 (14)°, and by 80.85 (13) and 79.62 (12)° to the mean plane of the piperidine ring. The terminal pyridine ring is inclined to the piperidine ring mean plane by 74.79 (15)°. In the crystal, mol­ecules are linked by C—H⋯π inter­actions, forming a three-dimensional network.

Spectral studies of 2-pyrazoline derivatives: structural elucidation through single crystal XRD and DFT calculations

A series of biologically active N-thiocarbamoyl pyrazoline derivatives have been synthesized using anhydrous potassium carbonate as the catalyst. All the synthesized compounds were characterized by FT-IR, (1)H NMR, (13)C NMR spectral studies, LCMS, CHN Analysis and X-ray diffraction analysis (compound 7). In order to supplement the XRD parameters, molecular modelling was carried out by Gaussian 03W. From the optimized structure, the energy, dipolemoment and HOMO-LUMO energies of all the systems were calculated.

1-[2-Hy-droxy-4-(prop-2-yn-1-yl-oxy)phen-yl]ethanone

In the title compound, C11H10O3, there is an intra-molecular O-H⋯O hydrogen bond generating an S(6) ring motif. The O atom of the hy-droxy group deviates by 0.0200 (1) Å from the benzene ring to which it is attached. The propyne group is almost linear, the C-C C angle being 177.83 (15)°, and is almost coplanar with the benzene ring; the C-C-O-C torsion angle being only -1.1 (2)°. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds, forming infinite C(11) chains running parallel to [103]. These chains are linked by a pair of C-H⋯O hydrogen bonds, enclosing R 2 (2)(8) inversion dimers, forming a corrugated two-dimensional network lying parallel to (103).

[(4E)-1-Methyl-2,6-diphenyl-3-(propan-2-yl)piperidin-4-yl-idene]amino 3-methyl-benzoate

In the title compound, C₂₉H₃₂N₂O₂, the piperidine ring exists in a chair conformation (the bond-angle sum at the sp²-hybridized C atom is 359.79°). The phenyl rings and the methyl group substituted on the heterocyclic ring are in equatorial orientations. In the crystal, pairs of C—H⋯π inter­actions result in the formation of inversion dimers.

[(4E)-3-Ethyl-1-methyl-2,6-di-phenyl-piperidin-4-yl-idene]amino 3-methyl-benzoate

In the title compound, C₂₈H₃₀N₂O₂, the piperidine ring exists in a chair conformation with an equatorial orientation of the phenyl rings and methyl group substituted on the heterocycle. In the crystal, C—H⋯π inter­actions result in chains of mol­ecules running parallel to the a-axis direction.

Crystal structure analysis of L-fuculose-1-phosphate aldolase from Thermus thermophilus HB8 and its catalytic action: as explained through in silico

Fuculose phosphate aldolase catalyzes the reversible cleavage of fuculose-1-phosphate to dihydroxyacetone phosphate and L-lactaldehyde. A tetramer by nature, this enzyme from Thermus thermophilus HB8 represents the group of Class II aldolases. The structure was solved in two different space groups using the crystals obtained from slow evaporation vapour-diffusion and microbatch techniques. The detailed crystallization description has been reported previously. In this study, the structural features of fuculose phosphate aldolase from T. thermophilus have been explored extensively through sequence and structure comparisons with fuculose phosphate aldolases of different species. Finally, an in silico analysis using induced fit docking was attempted to deduce the binding mode of fuculose phosphate aldolase with its natural substrate fuculose-1-phosphate along with a substrate analog dihydroxyacetone phosphate and phosphoglycolohydroxymate--a potential aldolase inhibitor. The results show the mechanism of action may be similar to that of Escherichia coli fuculose aldolase.

4-[2-(4-Butoxyphenyl)ethenyl]-1-methylpyridinium tosylate

In the title mol­ecular salt, C₁₈H₂₂NO⁺·C₇H₇O₃S⁻, the dihedral angle between the aromatic rings in the cation is 10.00 (9)°; its alkyl side chain adopts an extended conformation. In the crystal, weak C—H⋯O and π–π [centroid–centroid distance = 3.7658 (17) Å] inter­actions link the components, generating a three-dimensional network.

Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences

Background

Comparison of short peptides which form amyloid-fibrils with their homologues that may form amorphous β-aggregates but not fibrils, can aid development of novel amyloid-containing nanomaterials with well defined morphologies and characteristics. The knowledge gained from the comparative analysis could also be applied towards identifying potential aggregation prone regions in proteins, which are important for biotechnology applications or have been implicated in neurodegenerative diseases. In this work we have systematically analyzed a set of 139 amyloid-fibril hexa-peptides along with a highly homologous set of 168 hexa-peptides that do not form amyloid fibrils for their position-wise as well as overall amino acid compositions and averages of 49 selected amino acid properties.

Results

Amyloid-fibril forming peptides show distinct preferences and avoidances for amino acid residues to occur at each of the six positions. As expected, the amyloid fibril peptides are also more hydrophobic than non-amyloid peptides. We have used the results of this analysis to develop statistical potential energy values for the 20 amino acid residues to occur at each of the six different positions in the hexa-peptides. The distribution of the potential energy values in 139 amyloid and 168 non-amyloid fibrils are distinct and the amyloid-fibril peptides tend to be more stable (lower total potential energy values) than non-amyloid peptides. The average frequency of occurrence of these peptides with lower than specific cutoff energies at different positions is 72% and 50%, respectively. The potential energy values were used to devise a statistical discriminator to distinguish between amyloid-fibril and non-amyloid peptides. Our method could identify the amyloid-fibril forming hexa-peptides to an accuracy of 89%. On the other hand, the accuracy of identifying non-amyloid peptides was only 54%. Further attempts were made to improve the prediction accuracy via machine learning. This resulted in an overall accuracy of 82.7% with the sensitivity and specificity of 81.3% and 83.9%, respectively, in 10-fold cross-validation method.

Conclusions

Amyloid-fibril forming hexa-peptides show position specific sequence features that are different from those which may form amorphous β-aggregates. These positional preferences are found to be important features for discriminating amyloid-fibril forming peptides from their homologues that don't form amyloid-fibrils.

3-Hy-droxy-1-[(morpholin-4-yl)meth-yl]pyridazin-6(1H)-one

In the title compound, C₉H₁₃N₃O₃, the morpholine ring adopts a chair conformation and its mean plane makes a dihedral angle of 68.00 (11)° with the pyridazine ring. The carbonyl O atom deviates from the plane of the pyridazine ring by 0.0482 (12) Å. An intra­molecular C—H⋯O hydrogen bond occurs. In the crystal, mol­ecules are linked by O—H⋯O and C—H⋯O hydrogen bonds, forming chains along [1-10].

2-Hy-droxy-4-(prop-2-yn-yloxy)benz-alde-hyde

The asymmetric unit of the title compound, C₁₀H₈O₃, contains two independent mol­ecules, both of which are almost planar (r.m.s deviations for all non-H atoms of 0.044 and 0.053 Å). The dihedral angles between the benzene ring and the prop-1-yne group are 3.47 (1) and 3.07 (1)° in the two mol­ecules, and the prop-1-yne groups adopt extended conformations. In each mol­ecule, an intra­molecular O—H⋯O hydrogen bond involving the OH and aldehyde substituents forms an S(6) ring. In the crystal, mol­ecules are linked into cyclic centrosymmetric dimers via C—H⋯O hydrogen bonds, generating R₂²(14) ring motifs. The crystal structure is further stabilized by aromatic π–π stacking inter­actions between the benzene rings [centroid–centroid distances = 3.813 (2) and 3.843 (2) Å]

6-(4-Methoxyphenyl)naphtho[2,3-b][1]benzothiophene

The asymmetric unit of the title compound, C₂₃H₁₆OS, contains two independent mol­ecules with opposite orientations of the meth­oxy groups bonded to the benzene rings. The napthobenzothiophene group in the two molecules is separated by an average distance of 3.912 Å. In both mol­ecules, the napthobenzothio­phene unit is almost planar, with r.m.s deviations of 0.0522 and 0.0143 Å. The meth­oxy­phenyl ring makes dihedral angles of 67.0 (6)° and 70.4 (6)° with respect to the napthobenzothio­phene ring system in the two mol­ecules. The crystal packing features C—H⋯S, π–π [centroid–centroid distances = 3.666 (10) and 3.658 (10) Å] and C–H⋯π inter­actions, forming a sheet running along the b-axis direction.

6-Phenyl-benzo[d]naphtho-[2,3-b]thio-phene

In the title compound, C22H14S, the r.m.s. deviation from the mean plane of the four-fused-ring naphtho-thio-phene unit is 0.056 Å. The dihedral angle between the naphtho-thio-phene plane and the pendant phenyl ring is 67.24 (6)°. In the crystal, weak C-H⋯π and π-π stacking [minimum centroid-centroid separation = 3.7466 (10) Å] inter-actions are observed, which together lead to (010) sheets.

4-Ferrocenyl-1-methyl-3-benzoyl-spiro-[pyrrolidine-2,11'-indeno-[1,2-b]quinoxaline]

In the title compound, [Fe(C₅H₅)(C₃₁H₂₄N₃O)], the pyrrolidine ring adopts a twist conformation. The pyrrolidine ring is almost perpendicular to the indeno­quinoxaline ring system, making a dihedral angle of 84.44 (5)°. The cyclo­penta­dienyl rings of the ferrocene moiety adopt an eclipsed conformation. The crystal packing features weak C—H⋯N and C—H⋯π inter­actions.