Cp2ZrCl2: AN EFFICIENT CATALYST FOR MULTICOMPONENT SYNTHESIS OF CAROTENOID DEHYDROSQUALENE SYNTHASE INHIBITING PYRANO[2,3-d]PYRIMIDINEDIONES

Objectives: The present protocol deals with zirconocene dichloride (Cp2ZrCl2) catalyzed synthesis of pyrano[2,3-d]pyrimidinediones through one-pot multicomponent reactions of aromatic aldehydes with malononitrile and barbituric acid at ambient temperature. All the synthesized compounds were characterized and evaluated for antibacterial, antifungal, and antioxidant activities. Furthermore, a molecular docking was carried out to reveal the atomic insights between synthesized compounds and carotenoid dehydrosqualene synthase (PDB ID: 3ACX). Methods: All the synthesized compounds were evaluated for their in vitro antimicrobial activity by diffusion method. Antioxidant activities such as 1,1-diphenyl-2-picrylhydrazyl and radical scavenging activity. A mixture of barbituric acid 1 (1 mmol), malononitrile 2 (1 mmol), benzaldehyde 3a (1 mmol), ethanol (5 mL), and Cp2ZrCl2 (5 mol %) was stirred at ambient temperature for specified time. After completion of reaction as indicated by thin-layer chromatography, the obtained crude product was filtered and purified by column chromatography on silica gel (Merck, 60–120 mesh) using ethyl acetate:pet. ether to afford pure product which was then characterized by spectroscopic methods such by FTIR, nuclear magnetic resonance (1H NMR), 13C NMR, and mass spectroscopy. Results: All the synthesized pyrano[2,3-d]pyrimidinediones were characterized by spectroscopic analysis. The results revealed that pyrano[2,3-d] pyrimidinediones (4 a-k) displayed the zone of inhibition in the range of 3–13 mm. The most active compound 4b displayed largest zone of inhibition of 13 mm for Escherichia coli (NCIM-2832) and 9 mm for Bacillus subtilis (NCIM-2635). The antifungal and antioxidant activity of all synthesized pyrano[2,3-d]pyrimidinediones (4a-k) showed moderate to good activity. Molecular docking studies suggest that pyrano[2,3-d]pyrimidinediones might inhibit the carotenoid dehydrosqualene synthase activity. Conclusion: All the synthesized pyrano[2,3-d]pyrimidinediones display moderate to good antibacterial, antifungal, and antioxidant activity. This molecular docking studies supported that pyrano[2,3-d]pyrimidinediones might inhibit the carotenoid dehydrosqualene synthase (PDB ID: 3ACX)

Probing the Outer Mouth Structure of the hERG Channel with Peptide Toxin Footprinting and Molecular Modeling

Abstract Previous studies have shown that the unusually long S5-P linker lining human ether a-go-go related gene’s (hERG’s) outer vestibule is critical for its channel function: point mutations at high-impact positions here can interfere with the inactivation process and, in many cases, also reduce the pore’s K+ selectivity. Because no data are available on the equivalent region in the available K channel crystal structures to allow for homology modeling, we used alternative approaches to model its three-dimensional structure. The first part of this article describes mutant cycle analysis used to identify residues on hERG’s outer vestibule that interact with specific residues on the interaction surface of BeKm-1, a peptide toxin with known NMR structure and a high binding affinity to hERG. The second part describes molecular modeling of hERG’s pore domain. The transmembrane region was modeled after the crystal structure of KvAP pore domain. The S5-P linker was docked to the transmembrane region based on data from previous NMR and mutagenesis experiments, as well as a set of modeling criteria. The models were further restrained by contact points between hERG’s outer vestibule and the bound BeKm-1 toxin molecule deduced from the mutant cycle analysis. Based on these analyses, we propose a working model for the open conformation of the outer vestibule of the hERG channel, in which the S5-P linkers interact with the pore loops to influence ion flux through the pore

Characterization of the algC

Relative quantification of algC gene expression was evaluated in the multidrug resistant strain Acinetobacter baumannii AIIMS 7 biofilm (3 to 96 h, on polystyrene surface) compared to the planktonic counterparts. Comparison revealed differential algC expression pattern with maximum 81.59-fold increase in biofilm cells versus 3.24-fold in planktonic cells (P<0.05). Expression levels strongly correlated with specific biofilm stages (scale of 3 to 96 h), coinciding maximum at initial surface attachment stage (9 h) and biofilm maturation stage (48 h). Cloning, heterologous expression, and bioinformatics analyses indicated algC gene product as the bifunctional enzyme phosphomannomutase/phosphoglucomutase (PMM/PGM) of ∼53 kDa size, which augmented biofilms significantly in algC clones compared to controls (lacking algC gene), further localized by scanning electron microscopy. Moreover, molecular dynamics analysis on the three-dimensional structure of PMM/PGM (simulated up to 10 ns) revealed enzyme structure as stable and similar to that in P. aeruginosa (synthesis of alginate and lipopolysaccharide core) and involved in constitution of biofilm EPS (extracellular polymeric substances). Our observation on differential expression pattern of algC having strong correlation with important biofilm stages, scanning electron-microscopic evidence of biofilm augmentation taken together with predictive enzyme functions via molecular dynamic (MD) simulation, proposes a new basis of A. baumannii AIIMS 7 biofilm development on inanimate surfaces

ANTIBACTERIAL ACTIVITY OF VULGAROL A EXTRACTED FROM THE LEAVES OF SYZYGIUM CUMINI

Objectives: Extraction, purification and identification of antimicrobial compounds from leaves of Syzygium cumini.  Methods: The antibacterial activity of crude extract of Syzygium cumini leaves were investigated against pathogenic Gram positive and Gram negative bacteria. Petroleum ether extract was used for the separation of compound using thin layer chromatography and separated compound identified by using Gas Chromatography-Mass Spectroscopy.Results:Extracts prepared in various organic solvents such as chloroform, methanol, petroleum ether, acetone and ethanol showing antibacterial activity against Salmonella typhimurium, Pseudomonas aeruginosa and Staphylococcus aureus, but significant activity found with petroleum ether extract. The purified compound from petroleum ether extract showing antibacterial activity was identified as diterpenoids i.e. Vulgarol A by Gas Chromatography-Mass Spectroscopy. Vulgarol A shows more potential antibacterial activity against Gram negative organisms such as P. aeruginosa.Conclusion:This study concludes that the extracted compound Vulgarol A from Syzygium cumini leaves could be used as an active pharmaceutical ingredient to control infectious diseases caused by P. aeruginosa. Keywords: Syzygium cumini, diterpenoids, P. aeruginosa, GC-M

Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach.

Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by 'wobble' as well as a novel 'single' hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons

Hydrogen bonding interactions of τm⁵U.

<p>Hydrogen bonding interactions of τm⁵U.</p

Base pairing interactions of UUG codon and ASL anticodon of tRNA^Leu in the context of ribosomal A-site residues.

<p>Base pairing interactions of UUG codon and ASL anticodon of tRNA^Leu in the context of ribosomal A-site residues.</p

Initial structure of 55S ribosomal A-site residues (spring green color) along with ASL of tRNA^Leu (magenta color) with mRNA codon UUG (orange red color) considered for MD simulations.

<p>Initial structure of 55S ribosomal A-site residues (spring green color) along with ASL of tRNA^Leu (magenta color) with mRNA codon UUG (orange red color) considered for MD simulations.</p

Hydrogen bonding interactions of ribosomal A-site residues (A918, A919 and G256) with ASL of tRNA^Leu and mRNA codon UUG.

<p>Hydrogen bonding interactions of ribosomal A-site residues (A918, A919 and G256) with ASL of tRNA^Leu and mRNA codon UUG.</p