Showing papers by "Ponnurengam Malliappan Sivakumar published in 2012"

Green Synthesis of Protein Stabilized Silver Nanoparticles Using Pseudomonas fluorescens, a Marine Bacterium, and Its Biomedical Applications When Coated on Polycaprolactam

Abstract: Green synthesis of protein stabilized silver nanoparticles (AgNPs) using the supernatant of a marine isolate, Pseudomonas fluorescens PMMD3 (P.fluorescens), and its biomedical applications and bioc...

QSAR studies on substituted 3- or 4-phenyl-1,8-naphthyridine derivatives as antimicrobial agents

Abstract: Quantitative Structure Activity Relationship correlating the antitubercular and antibacterial (Staphylococcus aureus and Escherichia coli) activities with the structural descriptors of reported naphthyridine derivatives was developed. The data were divided into training and test sets. The former was used to develop the regression model and the latter was used to examine the predictive capability of these models. The statistical measures such as squared correlation coefficient (r2 = 0.79–0.84), adjusted squared correlation coefficient (r2adj = 0.78–0.83) F-ratio (26.85–67.16), and cross-validation (q2 = 0.74–0.79) were found to be satisfactory for all activities and the predictions were within the 99% confidence level. The models contained atom type, thermodynamic, structural, and electrotopological descriptors which emphasized the importance of the size, shape, and the lipophilicity of the molecule.

Antibacterial activities of 4-substituted-2-[(E)-{(1S,2R)/(1R,2S)-1-hydroxy-1-phenylpropan-2-ylimino}methyl]phenol

Abstract: A series of norephedrine-based Schiff bases (1a–6a and 1b–6b) were synthesized by reacting substituted salicylaldehydes with d-norephedrine or l-norephedrine. The structure of these compounds was confirmed by elemental analyses and spectroscopic techniques. The molecular structures of 5a and 6a have been determined by X-ray crystallography, which revealed that the compounds are in the oxoamino form, with bent intramolecular N-H···O (N···O ≈ 2.58 A) hydrogen bonds and that they are associated in dimers bridged by linear intermolecular O-H···O (O···O ≈ 2.69 A) hydrogen bonds. The density functional theory calculations on 5a confirmed that the oxoamino form is more stable than the phenolimino form by 12.2 kcal/mol. All the compounds were evaluated for their antibacterial activity using resazurin dye as indicator by twofold dilution method against four bacteria namely, Bacillus subtilis (NCIM2718), Staphylococcus aureus (NCIM5021), Escherichia coli (NCIM2931), and Proteus vulgaris (NCIM2813).

Computational approaches to enhance activity of taxanes as antimitotic agent

Abstract: Eighty semisynthetic taxanes were used to develop a quantitative structure activity relationship (QSAR) and also dock with the microtubule assembly and develop a relationship between binding energy and activity. These two equations could be used to predict activity of new taxanes. The data collected from literature were divided into training (61) and test (19) sets and the former were used to develop the equation. In the QSAR, topological, hydrophobic, and structural descriptors are found to be the major contributors of activity. The statistical parameters r 2 (0.72), $$ r_{\text{adj}}^{2} $$ (0.69), q 2 (0.65), and F ratio (23.26) were found to be satisfactory and the predictions were with in the 99% confidence interval. The docking studies of taxanes (using training set compounds) using microtubule (PDB: 1JFF) shows that the binding energy is negatively correlated with the antimicrotubule activity (r = −0.66). Hydrogen bond is found to be predominant factor for the binding of the taxanes with the microtubule. The relationship between binding energy and activity (r 2 (0.72), $$ r_{\text{adj}}^{2} $$ (0.69), q 2 (0.65), and F ratio (23.26)) was able to predict the data in the test set within the 99% confidence limits. In addition, these theoretical studies will give additional inputs to the medicinal chemists to design newer and potent taxane derivatives as antimitotic agents.

Computational Approaches to Improve Aggrecanase-1 Inhibitory Activity of (4-keto) Phenoxy) Methyl Biphenyl-4-sulfonamide: Group Based QSAR and Docking Studies

Abstract: Group based Quantitative Structure Activity Relationship (GQSAR) was developed for thirty (4-keto-phenoxy) methyl biphenyl-4-sulfonamides which exhibit aggrecanase-1 enzyme inhibitory activity. This enzyme is involved in osteoarthritis. The data is divided into training and test sets, where the latter is used for validating the model. Substitution in the R1 position plays a major role when compared to substitution in R2 position. The former position is influenced by two descriptors, namely electrotopological and connectivity indices. R2 position is influenced by radius of gyration. The statistical parameters for the training set (r2 = 0.80, r2adj = 0.77, q2 = 0.69, F-ratio = 26.80 and standard error = 0.24) and the predicted r2 (r2 test =0.95) are satisfactory. Docking of the compounds with aggrecanase-1 enzyme showed that there is a strong negative correlation between the binding energy and aggrecanase -1 inhibitory activity. Compounds with the carbonyl substitution interact with the S'1 pocket which is needed for enhanced activity. The two methodologies described here can help in lead optimization.