Prashantha Karunakar

Comparative Reverse Screening Approach to Identify Potential Anti-neoplastic Targets of Saffron Functional Components and Binding Mode

BACKGROUND In the last two decades, pioneering research on anti-tumour activity of saffron has shed light on the role of crocetin, picrocrocin and safranal, as broad spectrum anti-neoplastic agents. However, the exact mechanisms have yet to be elucidated. Identification and characterization of the targets of bioactive constituents will play an imperative role in demystifying the complex anti-neoplastic machinery. METHODS In the quest of potential target identification, a dual virtual screening approach utilizing two inverse screening systems, one predicated on idTarget and the other on PharmMapper was here employed. A set of target proteins associated with multiple forms of cancer and ranked by Fit Score and Binding energy were obtained from the two independent inverse screening platforms. The validity of the results was checked by meticulously analyzing the post-docking binding pose of the picrocrocin with Hsp90 alpha in AutoDock. RESULTS The docking pose reveals that electrostatic and hydrogen bonds play the key role in inter-molecular interactions in ligand binding. Picrocrocin binds to the Hsp90 alpha with a definite orientation appropriate for nucleophilic attacks by several electrical residues inside the Hsp90-alpha ATPase catalytic site. CONCLUSION This study reveals functional information about the anti-tumor mechanism of saffron bioactive constituents. Also, a tractable set of anti-neoplastic targets for saffron has been generated in this study which can be further authenticated by in vivo and in vitro experiments.

The Sensor Region of the Ubiquitous Cytosolic Sensor Kinase, Pdtas, Contains Pas and Gaf Domain Sensing Modules.

Two-component systems, a sensor histidine kinase (HK) and a response regulator (RR), are ubiquitous signaling systems that allow prokaryotes to respond to external challenges. HKs normally have sensing modules and highly conserved cytosolic histidine kinase and ATPase domains. The interaction between the activated phosphohistidine and the cognate RR allows an external signal to be passed from the exterior of gram-positive bacteria (GPB) to the cytoplasm. Orthologs of the PdtaS/PdtaR regulatory system, found in most GPB phyla, are unusual in two respects. The HK is not membrane anchored, and the RR acts at the level of transcriptional antitermination. The structure of the complete sensor region of the cytosolic HK, PdtaS, from Mycobacterium tuberculosis consists of closely linked GAF and PAS domains. The structure and sequence analysis suggest that the PdtaS/PdtaR regulatory system is structurally equivalent to the EutW/EutV system regulating ethanolamine catabolism in some phyla but that the effector for the PAS domain is not ethanolamine in the Actinobacteria.

Molecular interaction of fenvalarate with actin.

The structure of α-Cyano-3-phenoxybenzyl-2-(4-chlorophenyl)-3-methylbutyrate (Fenvalarate) has been established by X-ray crystallography to understand the structure-activity relationship, which is of paramount importance in the toxicological studies of the compound. Fenvalarate is stabilized by intermolecular C-H…O, C-H…Cl, C-H…π and C-H…N interactions which are responsible for the stability of the compound and its interaction with the Actin. The crystallographic coordinates of the compound was extrapolated to docking studies to elucidate the action of fenvalarate against neural cytoskeletal protein of insect and mammalian β-actin. A strong affinity was observed in binding of fenvalarate with insect β-actin (7.71kcal/mol, Ki = 2.23µM) indicating it as a potent insecticide and moderate toxicity towards mammalian β-actin (7.07kcal/mol, Ki=6.54µM).

In silico antitubercular activity analysis of benzofuran and naphthofuran derivatives.

For the human health, Mycobacterium tuberculosis (MTB) is the deadliest enemy since decades due to its multidrug resistant strains. During latent stage of tuberculosis infection, MTB consumes nitrate as the alternate mechanism of respiration in the absence of oxygen, thus increasing its survival and virulence. NarL is a nitrate/nitrite response transcriptional regulatory protein of two-component signal transduction system which regulates nitrate reductase and formate dehydrogenase for MTB adaptation to anaerobic condition. Phosphorylation by sensor kinase (NarX) is the primary mechanism behind the activation of NarL although many response regulators get activated by small molecule phospho-donors in the absence of sensor kinase. Using in silico approach, the molecular docking of benzofuran and naphthofuran derivatives and dynamic study of benzofuran derivative were performed. It was observed that compound Ethyl 5-bromo-3-ethoxycarbonylamino-1-benzofuran-2-carboxylate could be stabilized at the active site for over 10 ns of simulation. Here we suggest that derivatives of benzofuran moiety can lead to developing novel antituberculosis drugs.

Inhibition of NarL of Mycobacterium Tuberculosis: an in silico approach

Mycobacterium tuberculosis (MTB) consumes nitrate as the alternate mechanism of respiration in the absence of oxygen, thus increasing its survival and virulence during latent stage of tuberculosis infection. NarL is a nitrate/nitrite response transcriptional regulatory protein of two-component signal transduction system which regulates nitrate reductase and formate dehydrogenase for MTB adaptation to anaerobic condition. Phosphorylation by sensor kinase (NarX) is the primary mechanism behind the activation of NarL although many response regulators get activated by small molecule phospho-donors in the absence of sensor kinase. Virtual screening was performed using Autodock suite for the compounds from ZINC database against NarL and potential inhibitors was identified to inhibit the activation of NarL by affecting its phosphorylation. Molecular dynamics simulation studies predicted the stability of 1-{1-[(3-nitrophenyl) methyl] piperidin-2-yl} ethan-1-amine in the active site of NarL over 10 ns simulation. Phosphorylation of NarL by small molecule phospho-donors is also investigated in the present study. Here we suggest that nitro benzene - amine piperidine moiety can be an effective lead candidate for developing novel anti-tuberculosis drugs.

Effect of Structural Changes in Proteins Derived from GATA4 Nonsynonymous Single Nucleotide Polymorphisms in Congenital Heart Disease

Congenital heart disease is the most common type of birth defect. The single nucleotide polymorphism in GATA4 is associated with various congenital heart disease phenotypes. In the present study, we analysed the nonsynonymous single nucleotide polymorphism of GATA4, which are involved in congenital heart disease by predicting the changes in protein structures. Total of 49 nonsynonymous single nucleotide polymorphisms of GATA4 was screened from congenital heart disease patients of Mysore and also globally reported nonsynonymous single nucleotide polymorphisms. To understand the role of nonsynonymous single nucleotide polymorphisms, we mutated the sequence and translated into amino acids. Further the mutated protein secondary structure is predicted and tertiary structure is predicted using homology modeling. The quantitative evaluation of protein structure quality was verified with Volume Area Dihedral Angle Reporter server. Results revealed the secondary, tertiary structural changes along with changes in free energy of folding, volume and accessible surface area. Thus, the structural changes in the mutated proteins impaired the normal function of GATA4.