On the topological evidences for modelling lipophilicity

Topological evidences for modelling lipophilicity of a large series of diversed compounds have been provided on the basis of distance-based topological indices. A pool of topological indices along with indicator parameters related to the type of the compounds present in the set of 140 compounds were used for this purpose. The results have shown that topology as well as the type of compounds are the responsible parameters for modelling lipophilicity.     

QSAR studies on benzene sulfonamide carbonic anhydrase inhibitors: need of hydrophobic parameter for topological modeling of binding constants of sulfonamides to human CA-II

The binding constants (logK) of benzene sulfonamides to human CA-II have been modeled using a large series of distance-based topological indices. The need or otherwise of the hydrophobic parameter (logP) for such topological modeling of logK has been examined critically. In both the cases excellent results have been obtained. In multiparametric models involving indicator parameters we observed that introduction of hydrophobic parameter (logP) yields much improved statistics. The results are discussed on the basis of statistical parameters and also by using cross-validation method.     

Quantitative structure-activity relationship study on sulfanilamide schiff's bases: carbonic anhydrase (CA) inhibitors

The paper deals with quantitative structure–activity studies on a group of sulfanilamide Schiff's base inhibitors of carbonic anhydrase (CA) using distance-based topological indices. The regression analysis of the data has shown that the activities of the compounds used in inhibiting Carbonic AnhydraseII (CAII) activity can be modeled excellently in multi-parametric model in that some indicator parameters are also involved. The results are discussed critically.     

QSAR studies on carbonic anhydrase inhibitors: a case of ureido and thioureido derivatives of aromatic/heterocyclic sulfonamides

QSAR studies on modelling of biological activity (hCAI) for a series of ureido and thioureido derivatives of aromatic/heterocyclic sulfonamides have been made using a pool of topological indices. Regression analysis of the data showed that excellent results were obtained in multiparametric correlations upon introduction of indicator parameters. The predictive abilities of the models are discussed using cross-validation parameters.     

QSAR study on (13)C NMR chemical shifts on carbinol carbon atoms

QSAR calculations of (13)C NMR chemical shifts (ppm, TMS=0) on carbinol carbon atoms have been attempted using a large set of distance based topological indices: Wiener (W)-, Szeged (Sz)-, PI (Padmakar-Ivan) and Connectivity ((m)chi, (m)chi(v)) indices. The regression analysis has shown that excellent results are obtained in multiparametric regression. The predictive power of the proposed models are discussed using cross-validated parameters.     

Topological approach to quantifying molecular lipophilicity of heterogeneous set of organic compounds

The lipophilicity of the large set of organic compounds is investigated using distance-based topological indices. The results have shown that molecular lipophilicity can be modeled in multi-parametric model in that W, 1 chi, B, J and logRB along with indicator parameters are involved. The results are discussed critically.     

Succinctly assessing the topological importance of species in flower–pollinator networks

The topological importance of species within networks is an important way of bringing a species-level consideration to the study of whole ecological networks. There are many different indices of topological importance, including centrality indices, but it is likely that a small number are sufficient to explain variation in topological importance. We used 14 indices to describe topological importance of plants and pollinators in 12 quantitative mutualistic (plant–pollinator) networks. The 14 indices varied in their consideration of interaction strength (weighted versus unweighted indices) and indirect interactions (from the local measure of degree to meso-scale indices). We use principal components approximation to assess how well every combination of 1–14 indices approximated to the results of principal components analysis (PCA). We found that one or two indices were sufficient to explain up to 90% of the variation in topological importance in both plants and pollinators. The choice of index was crucial because there was considerable variation between the best and the worst approximating subsets of indices. The best single indices were unweighted degree and unweighted topological importance (Jordán's TI index) with two steps (a measurement of apparent competition). The best pairs of indices consisted of a measure of a TI index and one of closeness centrality (weighted or unweighted) or d′ (a standardised species-level measure of partner diversity). Although we have found indices that efficiently explain variation in topological importance, we recommend further research to discover the real-world relevance of different aspects of topological importance to species in ecological networks.     

Topological designing of 4-piperazinylquinazolines as antagonists of PDGFR tyrosine kinase family

Topological designing of a series of 4-piperazinylquinazolines as antagonists of platelet-derived growth factor receptor (PDGFR) tyrosine kinase family has been reported using a series of distance-based topological indices. Regression analysis of the data, using maximum R(2) method indicated that inhibitory activity, pIC(50) (microm), in cellular PGDFR phosphorylation assay can be modelled excellently in multi-parametric model. The results are discussed critically using cross-validated parameters.     

Quantitative structure-activity relationship studies on 5-phenyl-3-ureido-1,5-benzodiazepine as cholecystokinin-A receptor antagonists

Quantitative structure-activity relationship (QSAR) studies on a series of 5-phenyl-3-ureido-1,5-benzodiazepine-2,4-diones has been carried out using a pool of distance-based topological indices. Step-wise regression analysis indicated that penta-parametric regression expression containing Sz, B, Ip1, Ip2 and Ip3 is the most potent and selective for CCK-A affinity. The predictive potential of the model is discussed on the basis of cross-validation parameters as well as by estimating root mean square (RMSR) of the residuals.     

The root structures of 21 aquatic plants in a macrophyte-dominated lake in China

Aims Aquatic plants play an important role in freshwater ecosystems. Previous works have largely focused on the functional significance of plant above ground parts, with much less attention on the root structures of aquatic plants. In this study, we divided 21 aquatic plants (including five introduced plants) into multiple plant groups (different life forms, monocot/eudicot and introduced/native) with the goal of addressing two questions: (i) what root structures do aquatic plants exhibit, and (ii) are there differences among these plant groups?Methods Twenty-one aquatic plants belonging to four life forms (free-floating, emergent, floating-leaved and submerged) were collected at the near flowering stage from a typical macrophyte-dominated lake in the Yangtze River Basin, China. The following root topological parameters were quantified: altitude (a), path length (p e), magnitude (M), mean topological length (b), topological index (TI) and normed indices q a and q b .Important findings The root topological indices TI, q a and q b for the 21 aquatic plants were 0.724 ± 0.013, 0.290 ± 0.031 and 0.152 ± 0.024 (means ± S.E.), respectively, revealing a general pattern of dichotomous branching, except for the aquatic root of Myriophyllum aquaticum (Vell.) Verdc., which displays herringbone branching. All three topological indices were significantly lower for monocots (TI = 0.700 ± 0.130, q a = 0.191 ± 0.149 and q b = 0.086 ± 0.236) than eudicots (TI = 0.752 ± 0.206, q a = 0.405 ± 0.569 and q b = 0.229 ± 0.393), indicating that the roots of monocots are typically more dichotomous-like than those of eudicots. Among the four life forms, the three topological indices for emergent plants (TI = 0.832 ± 0.006, q a = 0.616 ± 0.018 and q b = 0.381 ± 0.014) were significantly higher than those of the other three life forms. Overall, there was no difference between the topological indices of introduced and native aquatic plants, but the introduced species M. aquaticum and Alternanthera philoxeroides (Mart.) Griseb. had both aquatic and edaphic roots as well as unusual functions, which may help explain their strong viability.     

Topological modeling of lipophilicity, diuretic activity, and carbonic inhibition activity of benzene sulfonamides: a molecular connectivity approach

A large series of distance-based topological indices has been used for modeling lipophilicity, diuretic activity, and carbonic anhydrase inhibition activity of a library of simple substituted benzene sulfonamides. The results have shown that the topological approach used is quite useful for modeling carbonic anhydrase inhibition and the use of molecular connectivity is the best for this purpose. Excellent results are obtained in multiparametric regressions. The results are critically discussed on the basis of statistical parameters.     

QSAR studies on biological activity of piritrexim analogues against pc DHFR

Quantitative structure-activity relationship (QSAR) studies for 2,6-substituted 2,4-diaminopyrido[3,2-d] pyrimidine analogues of piritrexim (PTX) as inhibitors of dihydrofolate reductase (DHFR) are now made using topological indices. The results have shown that best models are obtained by multiparametric analysis. The predictive potential of the model is discussed on the basis of a cross-validation method.     

QSAR study on toxicity to aqueous organisms using the PI index

We have attempted to develop quantitative structure-toxicity relationships (QSTRs) to predict hydrophobicity (logP) as well as toxicity (pEC50 microm) of benzene derivatives using recently introduced Padmakar-Ivan (PI) index. The results have shown that both logP as well as pEC50 of benzene derivatives can be modelled excellently in multiparametric models in that the PI index and some indicator parameters are involved. The predictive ability of the models is discussed on the basis of the cross-validation method. The superiority of the PI index over several other topological indices is critically examined.     

Topological estimation of electronic absorption bands of arene absorption spectra as a tool for modeling their toxicity and environmental pollution

A novel application of distance-based topological indices : Wiener (W)-, Szeged (Sz)-, Padmakar-Ivan (PI)-, and Sadhana (Sd)-indices in modeling electronic absorption bands of arene absorption spectra has been described. It is demonstrated that all these indices correlate linearly with the logarithm of beta and para electronic absorption bands in several series of arene systems. The results have shown that our methodology is best suited for the estimation--lnlambda(beta), while comparatively less significant results are obtained in case of the estimation of lnlambda(p). The statistical analysis of the data have shown that PI index gives better results for modeling lnlambda(beta); while Sz index proved better for modeling lnlambda(p). The results are critically discussed on the basis of regression parameters and quality of correlation. Such a study will be useful as a tool for modeling toxicity of arene system as well as their environmental pollution.     

Naïve Bayes QSDR classification based on spiral-graph Shannon entropies for protein biomarkers in human colon cancer

Fast cancer diagnosis represents a real necessity in applied medicine due to the importance of this disease. Thus, theoretical models can help as prediction tools. Graph theory representation is one option because it permits us to numerically describe any real system such as the protein macromolecules by transforming real properties into molecular graph topological indices. This study proposes a new classification model for proteins linked with human colon cancer by using spiral graph topological indices of protein amino acid sequences. The best quantitative structure-disease relationship model is based on eleven Shannon entropy indices. It was obtained with the Na?ve Bayes method and shows excellent predictive ability (90.92%) for new proteins linked with this type of cancer. The statistical analysis confirms that this model allows diagnosing the absence of human colon cancer obtaining an area under receiver operating characteristic of 0.91. The methodology presented can be used for any type of sequential information such as any protein and nucleic acid sequence.