R. Priya

Phylogenetic analysis and evolutionary studies of plant carotenoid cleavage dioxygenase gene.

The oxidative breakdown of carotenoid evidences the formation of apocarotenoids through carotenoid cleavage dioxygenases (CCDs). Numerous CCDs and apocarotenoids have been identified and characterized in plants. Using available sequence data, a study was performed to investigate the phylogenetic relationship among CCD genes and to statistically estimate the sequence conservation and functional divergence. In total, 77 genes were identified from 39 species belonging to 21 families. Our result of phylogenetic analysis indicated the existence of well-conserved subfamilies. Moreover, comparative genomic analysis showed that the gene structures of the CCDs were highly conserved across some different lineage species. Through functional divergence analysis, a substantial divergence was found between CCD subfamilies. In addition, examination of the site-specific profile revealed the critical amino acid residues accounting for functional divergence. This study mainly focused on the evolution of CCD genes and their functional divergence which may deliver an initial step for further experimental verifications.

Inhibitory effect of apocarotenoids on the activity of tyrosinase : Multi-spectroscopic and docking studies

In this present study, the inhibitory mechanism of three selected apocarotenoids (bixin, norbixin and crocin) on the diphenolase activity of tyrosinase has been investigated. The preliminary screening results indicated that apocarotenoids inhibited tyrosinase activity in a dose-dependent manner. Kinetic analysis revealed that apocarotenoids reversibly inhibited tyrosinase activity. Analysis of fluorescence spectra showed that apocarotenoids quenched the intrinsic fluorescence intensity of the tyrosinase. Further, molecular docking results implied that apocarotenoids were allosterically bound to tyrosinase through hydrophobic interactions. The results of the in vitro studies suggested that higher concentrations of bixin and norbixin inhibited tyrosinase activity in B16F0 melanoma cells. Our results suggested that apocarotenoids could form the basis for the design of novel tyrosinase inhibitors.

Analysis of phylogenetic and functional diverge in plant nine‑cis epoxycarotenoid dioxygenase gene family

During different environmental stress conditions, plant growth is regulated by the hormone abscisic acid (an apocarotenoid). In the biosynthesis of abscisic acid, the oxidative cleavage of cis-epoxycarotenoid catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED) is the crucial step. The NCED genes were isolated in numerous plant species and those genes were phylogenetically investigated to understand the evolution of NCED genes in various plant lineages comprising lycophyte, gymnosperm, dicot and monocot. A total of 93 genes were obtained from 48 plant species to statistically estimate their sequence conservation and functional divergence. Selaginella moellendorffii appeared to be evolutionarily distinct from those of the angiosperms, insisting the substantial influence of natural selection pressure on NCED genes. Further, using exon–intron structure analysis, the gene structures of NCED were found to be conserved across some species. In addition, the substitution rate ratio of non-synonymous (Ka) versus synonymous (Ks) mutations using the Bayesian inference approach, depicted the critical amino acid residues for functional divergence. A significant functional divergence was found between some subgroups through the co-efficient of type-I functional divergence. Our results suggest that the evolution of NCED genes occurred by duplication, diversification and exon intron loss events. The site-specific profile and functional diverge analysis revealed NCED genes might facilitate the tissue-specific functional divergence in NCED sub-families, that could combat different environmental stress conditions aiding plant survival.

Studies on interaction of norbixin with DNA: Multispectroscopic and in silico analysis

The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08×10(5) Mol(-1) L. FTIR and CD studies were coupled with (1)H NMR spectra revealed that norbixin intercalates partially and binds to the grooves, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic.

Synthesis of 4-Hydroxy-2(1H)-Quinolone Derived Chalcones, Pyrazolines and Their Antimicrobial, In Silico Antimalarial Evaluations

A few derivatives of 3-(4,5-dihydro-5-aryl-1-phenyl-1H-pyrazol-3-yl)-4-hydroxyquinolin-2(1H)-ones (5a–j) that are synthesized from 4-hydroxy-3-(3-arylacryloyl)quinolin-2(1H)-ones (4a–j) by microwave-assisted synthesis are screened for their antimicrobial, in silico antimalarial activities. Among the tested compounds 4h and 5d were found to have a potent antimalarial activity than the standards, and the others are found to show considerable antimalarial activity and moderate antimicrobial activity.

Gene Expression Prediction and Hierarchical Clustering Analysis of Plant CCD genes

Plant carotenoid cleavage dioxygenase (CCD) catalyses the formation of industrially important apocarotenoids. Here, we applied codon-based classification for 72 CCD genes from 35 plant species using hierarchical clustering analysis. The codon adaptation index (CAI) and relative codon bias (RCB) were utilized to estimate the level of gene expression. The codon-based cluster tree result shows neatly clustered subclass of CCD genes except BoCCD1 gene of Bixa orellana. Correlation analysis of CAI values with RCB indicates an overall low-level expression of CCD across different species. Similarly, the closeness in the codon cluster with same CAI values was not reflected in 3-D structural report of selected CCD genes. These finding not only enhances our insights into the classification of CCD gene across the species but also identifies the critical factors responsible for this variation, which could aid in prediction of gene expression and function for newly reported CCD genes.

Evaluation of DNA Binding with Some Selected Hydrazide and Semicarbazide Derivatives

A group of hydrazide and semicarbazide derivatives containing isopropylidene, benzylidene, cyclohexylidene, and phospholidene groups was synthesized and characterized by spectroscopic techniques. These compounds were tested for DNA interaction studies monitored by UV-Vis and IR data as well as molecular docking. Investigations on interactions of these compounds with DNA revealed an intercalative mode of binding between them. It is interesting to note that semicarbazide derivatives with aliphatic substituents showed better DNA binding than the aromatic substituents.

Toxicity study of dibutyl phthalate of Rubia cordifolia fruits: in vivo and in silico analysis

Natural toxins from plant sources with wide ranges of biological activities reflect the upswing of drug design in the pharmaceutical industry. Rubia cordifolia L. is one of the most important red dye yielding plants. Most of the former researches have focused on the bioactive compounds from the roots of R. cordifolia, while no attention was paid towards the fruits. For the first time, here we report the presence of dibutyl phthalate in the fruits of R. cordifolia. Structural characterization was carried out using Ultraviolet–Visible spectrophotometer (UV–Vis), Fourier transform infrared (FTIR), gas chromatography–mass spectrophotometer (GC–MS), Nuclear magnetic resonance (NMR). Acute toxicity of the crude ethanolic extracts of the R. cordifolia fruits was examined in Swiss albino mice. No mortality was observed in all treated mice with 100, 500, 1000 mg/kg body weight of crude extract of R. cordifolia fruit and it indicates that the LD50 value is higher than 1000 mg/kg body weight. This study exhibited a significant change in the body weight. Alanine transaminase (ALT), total protein, triglycerides, glucose, and also the histopathological analysis of liver for all treated mice showed difference from the control group. The dibutyl phthalate was further evaluated for the toxicity study through in silico analysis. Together, the results highlighted that the toxic potential of R. cordifolia fruits extracts and also the toxicity profile of the fruit should be essential for the future studies dealing with the long term effect in animals.

Molecular Modeling and Dynamic Simulation of Arabidopsis thaliana Carotenoid Cleavage Dioxygenase Gene: A Comparison with Bixa orellana and Crocus sativus

Carotenoid cleavage dioxygenase (CCD) gene, ubiquitously found in numerous types of plants, are eminent in synthesizing the various volatile compounds (β‐ionone, C13‐norisoprenoid, geranylacetone) known as apocarotenoids. These apocarotenoids have various biological functions such as volatile signals, allelopathic interaction and plant defense. In Arabidopsis genome sequence, four potential CCD genes have been identified namely CCD1, CCD4, CCD7, and CCD8. These four genes give rise to diverse biological functions with almost similar sequence identity. In this investigation, an in silico analysis was proposed to study CCD proteins in Arabidopsis thaliana, aiming at constructing three‐dimensional (3D) structure for CCD1 proteins of Bixa orellana and Crocus sativus to observe the structural difference among AtCCD (A. thaliana CCD) proteins. The quality of modeled structures was evaluated using RAMPAGE, PSVS protein validation server and Q Mean server. Finally, we utilised molecular dynamics simulation to identify the stability of the predicted CCD protein structures. The molecular dynamic simulation also revealed that AtCCD4 protein showed lesser stability when compared to other CCD proteins. Overall results from molecular dynamics analysis predicted that BoCCD1, CsCCD1, and AtCCD1 show similar structural characteristics. J. Cell. Biochem. 118: 2712–2721, 2017.

Interaction of Catechu Dye with DNA: Spectroscopic and In Silico Approach

ABSTRACT Catechin, a yellow colored molecule obtained from the wood of Acacia catechu was analyzed for its interaction with synthetic DNA duplexes using spectroscopic analysis. UV-Visible spectroscopic analysis revealed the non-intercalative binding mode. Fourier Transform Infrared spectroscopy (FTIR) analysis expose chemical shift indicated by various vibrational stretches and an increase in the intensity of base stacking was observed by Circular Dichroism (CD), respectively. This inference was further confirmed through nuclear staining technique and also in electrophoretic technique; the dye quenches the fluorescent intensity of ethidium bromide. The result of fluorescence spectroscopy was in concordance with the electrophoretic technique. In addition, the spectroscopic results were in accordance with the molecular docking studies of specific catechin compound from the catechu dye with CT-DNA. This kind of site specificity is a gain in the medicinal field as the drug can be DNA targeted for cancer therapeutics. The present work reveals that catechu dye has a noteworthy application in the field of medical bioscience.