A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction

During last few decades accurate determination of protein structural class using a fast and suitable computational method has been a challenging problem in protein science. In this context a meaningful representation of a protein sample plays a key role in achieving higher prediction accuracy. In this paper based on the concept of Chou's pseudo amino acid composition (Chou, K.C., 2001. Proteins 43, 246-255), a new feature representation method is introduced which is composed of the amino acid composition information, the amphiphilic correlation factors and the spectral characteristics of the protein. Thus the sample of a protein is represented by a set of discrete components which incorporate both the sequence order and the length effect. On the basis of such a statistical framework a simple radial basis function network based classifier is introduced to predict protein structural class. A set of exhaustive simulation studies demonstrates high success rate of classification using the self-consistency and jackknife test on the benchmark datasets.     

Biophysical,spectroscopic vis-à-vis biochemical investigation on DNA–metalloprotein interaction: a model study involving cobalt(II)-glutathione complex

Abstract  The interaction of cobalt(II)-glutathione (CoGSH) with deoxyribonucleic acid (DNA) has been studied by UV–vis, fluorescence, circular dichroism (CD), thin-film infrared (IR), and viscometric techniques. From the UV-spectroscopic method, binding constant (K _b) was determined and was found to be 2.3 × 10⁶ M⁻¹. In fluorimetric analysis, the quenching of fluorescence intensity of DNA bound to ethidium bromide (EB) was investigated. The Stern–Volmer quenching constant (K _sv) was also estimated from this study and was found to be 2.8 × 10⁶ M⁻¹at 37 °C. The solution CD spectra of DNA and DNA–CoGSH indicate that in each case, DNA exists in the ‘B’ conformation and suggested an intercalative binding mode. Thin-film IR data also reveal that DNA attains the ‘B’ family of conformations after interaction with CoGSH complex. The increase in DNA viscosity in the presence of CoGSH complexes is attributed to the lengthening of DNA helix due to intercalation. Graphical Abstract  The spectrophotometric, CD, thin film IR, viscometric and fluorimetric studies on the interaction of CoGSH with DNA indicated an intercalative binding mode with the retention of ‘B’ conformation of DNA.      

Nuclear structure effects in parity non-conservation in heavy ions

We calculate the binding energy, charge radii in ¹²⁹Ba-¹⁴³Ba and ²¹⁴Ra-²²⁸Ra using the relativistic mean field theory which includes scalar and vector mesons. We then evaluate the nuclear structure corrections to the weak charges for a series of these isotopes using different parameters and estimate their uncertainty in the framework of this model. Our results will have important implication for the ongoing and planned parity nonconservation experiments and atomic structure calculations on Ba⁺ and Ra⁺.     

Tree 3-spanners in 2-sep chordal graphs: Characterization and algorithms

A spanning tree T of a graph G is said to be a treet-spanner if the distance between any two vertices in T is at most t times their distance in G. A graph that has a tree t-spanner is called a treet-spanner admissible graph. The problem of deciding whether a graph is tree t-spanner admissible is NP-complete for any fixed t≥4 and is linearly solvable for t≤2. The case t=3 still remains open. A chordal graph is called a 2-sep chordal graph if all of its minimal a−b vertex separators for every pair of non-adjacent vertices a and b are of size two. It is known that not all 2-sep chordal graphs admit tree 3-spanners. This paper presents a structural characterization and a linear time recognition algorithm of tree 3-spanner admissible 2-sep chordal graphs. Finally, a linear time algorithm to construct a tree 3-spanner of a tree 3-spanner admissible 2-sep chordal graph is proposed.     

Volatile Profiling of Magnolia champaca Accessions by Gas Chromatography Mass Spectrometry Coupled with Chemometrics

Magnolia champaca (L.) Baill. ex Pierre of family Magnoliaceae, is a perennial tree with aromatic, ethnobotanical, and medicinal uses. The M. champaca leaf is reported to have a myriad of therapeutic activities, however, there are limited reports available on the chemical composition of the leaf essential oil of M. champaca. The present study explored the variation in the yield and chemical composition of leaf essential oil isolated from 52 accessions of M. champaca. Through hydrodistillation, essential oil yield was obtained, varied in the range of 0.06 ± 0.003% and 0.31 ± 0.015% (v/w) on a fresh weight basis. GC-MS analysis identified a total of 65 phytoconstituents accounting for 90.23 to 98.90% of the total oil. Sesquiterpene hydrocarbons (52.83 to 65.63%) constituted the major fraction followed by sesquiterpene alcohols (14.71 to 22.45%). The essential oils were found to be rich in β-elemene (6.64 to 38.80%), γ-muurolene (4.63 to 22.50%), and β-caryophyllene (1.10 to 20.74%). Chemometrics analyses such as PCA, PLS-DA, sPLS-DA, and cluster analyses such as hierarchical clustering, i.e., dendrogram and partitional clustering, i.e., K-means classified the essential oils of M. champaca populations into three different chemotypes: chemotype I (β-elemene), chemotype II (γ-muurolene) and chemotype III (β-caryophyllene). The chemical polymorphism analyzed in the studied populations would facilitate the selection of chemotypes with specific compounds. The chemotypes identified in the M. champaca populations could be developed as promising bio-resources for conservation and pharmaceutical application and further improvement of the taxa.     

Modified Curcumins as Potential Drug Candidates for Breast Cancer: An Overview

Breast cancer (BC), the most common malignancy in women, results from significant alterations in genetic and epigenetic mechanisms that alter multiple signaling pathways in growth and malignant progression, leading to limited long-term survival. Current studies with numerous drug therapies have shown that BC is a complex disease with tumor heterogeneity, rapidity, and dynamics of the tumor microenvironment that result in resistance to existing therapy. Targeting a single cell-signaling pathway is unlikely to treat or prevent BC. Curcumin (a natural yellow pigment), the principal ingredient in the spice turmeric, is well-documented for its diverse pharmacological properties including anti-cancer activity. However, its clinical application has been limited because of its low solubility, stability, and bioavailability. To overcome the limitation of curcumin, several modified curcumin conjugates and curcumin mimics were developed and studied for their anti-cancer properties. In this review, we have focused on the application of curcumin mimics and their conjugates for breast cancer.     

Application of a Multilayer Perceptron Artificial Neural Network for the Prediction and Optimization of the Andrographolide Content in Andrographis paniculata

Andrographolide, the principal secondary metabolite of Andrographis paniculata, displays a wide spectrum of medicinal activities. The content of andrographolide varies significantly in the species collected from different geographical regions. Therefore, this study aims at investigating the role of different abiotic factors and selecting suitable sites for the cultivation of A. paniculata with high andrographolide content using a multilayer perceptron artificial neural network (MLP-ANN) approach. A total of 150 accessions of A. paniculata collected from different regions of Odisha and West Bengal in eastern India showed a variation in andrographolide content in the range of 0.28–5.45% on a dry weight basis. The MLP-ANN was trained using climatic factors and soil nutrients as the input layer and the andrographolide content as the output layer. The best topological ANN architecture, consisting of 14 input neurons, 12 hidden neurons, and 1 output neuron, could predict the andrographolide content with 90% accuracy. The developed ANN model showed good predictive performance with a correlation coefficient (R²) of 0.9716 and a root-mean-square error (RMSE) of 0.18. The global sensitivity analysis revealed nitrogen followed by phosphorus and potassium as the predominant input variables influencing the andrographolide content. The andrographolide content could be increased from 3.38% to 4.90% by optimizing these sensitive factors. The result showed that the ANN approach is reliable for the prediction of suitable sites for the optimum andrographolide yield in A. paniculata.     

Synthesis of Bicyclic N‐Methylpyrazoline and Pyrazole Derivatives from α,β‐Unsaturated Ketones and N,N‐Dimethylhydrazine: An Illustration of Reductive Cyclization

The reaction of N,N‐dimethylhydrazine with α,β‐unsaturated keto precursors such as 2‐benzylidenecyclohexanone, 2,6‐bis(benzylidene)cyclohexanone, and 3,5‐bis(benzylidene)‐1‐methyl‐4‐piperidone hydrochloride provided bicyclic N‐methylpyrazoles instead of hydrazones or any Michael addition products. The crystal structure of a representative pyrazole is reported. The proposed mechanism for the formation of the bicyclic N‐methylpyrazole 1 is outlined.     

Mn(III) and Cu(II) complexes of 1-((3-(dimethylamino)propylimino)methyl) naphthalen-2-ol): Synthesis,characterization, catecholase and phenoxazinone synthase activity and DFT-TDDFT study

Two new complexes, [MnL₂](ClO₄) (1) and [CuL₂] (2) (where LH = (E)-1-((3-(dimethylamino)propylimino)methyl)naphthalen-2-ol), have been synthesized and characterized by spectroscopic techniques and their molecular structures are established by single-crystal X-ray diffraction study. Complex 1 adopts an octahedral geometry around the central manganese atom which is in + 3 oxidation state, whereas in complex 2, the Cu⁺² ion preferred a square pyramidal environment around it through the ligand donor atoms. Both complexes were tested for catecholase and phenoxazinone synthase activity. Complex 1 catalyzes the oxidation of 3,5-ditertiary-butyl catechol with a k_cat value of 6.8424 × 10² h^?1 in acetonitrile whereas the same for complex 2 is 3.7485 × 10² h^?1 in methanol. Phenoxazinone synthase activity was shown only by complex 2 having k_cat = 74.225 h^?1. Structures of both the title complexes have been optimized by means of DFT calculations. Experimental electronic spectra of the complexes have been corroborated by TDDFT analysis. Electrochemical investigations by means of cyclic voltammetry have been carried out to study the electron transfer processes in the complexes.     

Binuclear metal complexes. Part III. Complexes of 1-hydroxy-2, 3-dimethyl-5-carboxylato-1,4-diaza-1,3-pentadiene and 1-hydroxy-2,3-dimethyl-4(2′-carboxyphenyl)-1,4-diaza-1, 3-butadiene with bivalent transition metal ion complexes

Summary Binuclear complexes of the type [M(HDCDP)(H₂O)_n]₂ and [M(HDCDB)(H₂O)_n]₂, where HDCDP and HDCDB are Schiff bases derived from glycine and diacetylmonoxime, and orthoaminobenzoic acid and diacetylmonoxime respectively, M=VO^II, Co^II, Ni^II, Cu^II or Ag^II and n=0 or 2, have been synthesized. Physical and spectroscopic analyses indicate a binuclear structure for the complexes with metal ions in an octahedral environment, where the ligands coordinate to the metal centre through azomethine nitrogens, oxime and carboxylate oxygen in a tetradentate manner.