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Biomedical subjects

S C Basak

Publications and source records attributed to S C Basak.

At least 37 records · Page 2Linked to original sources
PubMed1996

Characterization and immunoprotective properties of a monoclonal antibody against the major oocyst wall protein of Eimeria tenella.

The oocyst wall of Eimeria spp. consists of a 10-nm-thick outer lipid layer and a 90-mm-thick inner layer of glycoprotein which has been described previously to be composed of a single major protein. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions and (125)I labelling of a oocyst wall fragments and of delipidated intact oocysts revealed a molecule of approximately 12 kDa as the major protein component of the oocyst wall of Eimeria tenella. An immunoglobulin M monoclonal antibody (c11B9F3) was produced against this 12-kDa oocyst wall protein sliced from a preparative SDS-polyacrylamide gel. Its reactivity by immunofluorescence against oocyst wall fragments and sporozoites or by immunoperoxidase assays of infected tissue sections was stage restricted to gametocytes and oocysts but pan-specific against all face of the oocyst wall. In chicks passively immunized with C11B9F3, oocyst output was significantly (P<0.01) reduced by 42 to 54% after homologous E. tenella infection and by 35% after heterologous Eimeria maxima infection compared with that of control groups. The results demonstrate the presence of a highly conserved, low-molecular-weight antigen on the oocyst wall and the gametocytes of Eimeria spp. which is a candidate for inclusion in a pan-specific, transmission-blocking vaccine against avian coccidiosis.

Animals↗
PubMed1995

Predicting mutagenicity of chemicals using topological and quantum chemical parameters: a similarity based study.

Five molecular similarity methods have been used to estimate mutagenicity of a set of 73 aromatic and heteroaromatic amines. Two of the similarity methods (AP, PCTI) are based on topological parameters. Two other methods (PCPROP, PROP) are derived from physicochemical and electronic parameters. The fifth method, PCALL, is based on a combination of both topological and physicochemical parameters. The effectiveness of the five similarity methods in the rapid evaluation of mutagenicity is discussed.

Amines↗
PubMed1995

Use of graph theoretic parameters in risk assessment of chemicals.

In many instances of risk assessment, one has to estimate the potential risk of chemicals using limited experimental data, or no empirical data at all. In such cases, the use of non-empirical parameters, which can be calculated directly from structure, is a viable option for the risk assessor. Graph invariants have been used in predicting properties of congeneric sets of chemicals and determining structural similarity/dissimilarity of molecules. In this paper we have used (a) topological parameters in predicting mutagenicity of a diverse set of 520 chemicals and (b) graph theoretic parameters in quantifying structural similarity for a selection of analogs. The results of these analyses are presented along with a critical discussion of the utility and limitations of these methods.

Data Interpretation, Statistical↗
PubMed1995

Tolerance space and molecular similarity.

Molecular similarity methods were used in selecting K nearest neighbors and in estimating mutagenicity of 95 aromatic amines and boiling points of a large set of over 2,900 compounds. Similarity is analyzed in terms of the concept of tolerance space. Specifically, the role of non-transitivity of the tolerance relation in estimating properties using similarity methods is examined.

Amines↗
PubMed1984

Comparative study of lipophilicity versus topological molecular descriptors in biological correlations.

This paper analyzes the relative efficacies of lipophilicity vis-à-vis topological indices in the correlation of the biological properties of four groups of bioactive molecules: alcohols, barbiturates, triazinones , and ketobemidones . Wiener number (W), information-theoretic topological parameters (IC, SIC, CIC, IWD , and IWD ), and molecular connectivity indices (1 chi, 1 chi V) were used as the molecular descriptors. Results show that theoretical indices are comparable or superior to log P in biological correlations.

Alcohols↗
PubMed1983

Physicochemical and topological correlates of the enzymatic acetyltransfer reaction.

The relative potencies of a series of substituted anilines as acetyl acceptors in the enzymatic N-acetylation reaction have been correlated using physiochemical substituent constants (pi, sigma-), molecular connectivity indices (1 chi, 1 chi v), and newly formulated information-theoretic topological indices (IC, SIC). Results indicate a predominant role of the topological steric parameters in determining the rates of the N-acetyltransferase reaction.

Acetyltransferases↗
PubMed1982

Molecular connectivity and antifungal activity. A quantitative structure-activity relationship study of substituted phenols against skin pathogens.

The plot of minimum inhibitory concentration (MIC) vs. 2Xv of twelve phenolic compounds delineates the congeners into three distinct classes: the most potent ortho compounds describe a parabola, para substituted compounds of intermediate potency lie in a line, while the least potent meta derivatives yield a scatter diagram. The same pattern is found for two skin pathogens, Trichophyton rubrum and Epidermophyton floccosum. From non-linear regression analysis 2Xv is found to be excellently correlated with observed MIC values of the most potent ortho compounds against both the test organisms. For both the organisms logP is found to be inferior to 2Xv in the correlation of MIC values. On the basis of regression equations the MIC values of certain ortho substituted phenols are calculated a priori, some of which are corroborated by findings reported in the literature.

Antifungal Agents↗
PubMedDate not supplied

On 3-D graphical representation of DNA primary sequences and their numerical characterization.

In this article we (1) outline the construction of a 3-D "graphical" representation of DNA primary sequences, illustrated on a portion of the human beta globin gene; (2) describe a particular scheme that transforms the above 3-D spatial representation of DNA into a numerical matrix representation; (3) illustrate construction of matrix invariants for DNA sequences; and (4) suggest a data reduction based on statistical analysis of matrix invariants generated for DNA. Each of the four contributions represents a novel development that we hope will facilitate comparative studies of DNA and open new directions for representation and characterization of DNA primary sequences.

Base Sequence↗
PubMedDate not supplied

Comparison of a neural net-based QSAR algorithm (PCANN) with Hologram- and multiple linear regression-based QSAR approaches: application to 1,4-dihydropyridine-based calcium channel antagonists.

A QSAR algorithm (PCANN) has been developed and applied to a set of calcium channel blockers which are of special interest because of their role in cardiac disease and also because many of them interact with P-glycoprotein, a membrane protein associated with multidrug resistance to anticancer agents. A database of 46 1,4-dihydropyridines with known Ca2+ channel binding affinities was employed for the present analysis. The QSAR algorithm can be summarized as follows: (1) a set of 90 graph theoretic and information theoretic descriptors representing various structural and topological characteristics was calculated for each of the 1,4-dihydropyridines and (2) principal component analysis (PCA) was used to compress these 90 into the eight best orthogonal composite descriptors for the database. These eight sufficed to explain 96% of the variance in the original descriptor set. (3) Two important empirical descriptors, the Leo-Hansch lipophilic constant and the Hammet electronic parameter, were added to the list of eight. (4) The 10 resulting descriptors were used as inputs to a back-propagation neural network whose output was the predicted binding affinity. (5) The predictive ability of the network was assessed by cross-validation. A comparison of the present approach with two other QSAR approaches (multiple linear regression using the same variables and a Hologram QSAR model) is made and shows that the PCANN approach can yield better predictions, once the right network configuration is identified. The present approach (PCANN) may prove useful for rapid assessment of the potential for biological activity when dealing with large chemical libraries.

Algorithms↗
PubMedDate not supplied

Characterization of DNA primary sequences based on the average distances between bases.

We outline numerical characterization of DNA primary sequence based on calculation of the average distance between pairs of nucleic acid bases. This leads to a representation of DNA by a condensed 4 x 4 symmetrical matrix, the elements of which give the average separation between pair of bases X, Y in DNA (X, Y = A, C, G, T). As an invariant of choice we consider the leading eigenvalue of the derived 4 x 4 matrix. Additional structurally related invariants were obtained by constructing additional "higher order" 4 x 4 matrices derived from the initial 4 x 4 matrix by raising its elements to higher powers. Suitably normalized leading eigenvalue of these matrices offer a novel characterization of DNA primary sequences, referred to as "DNA profiles". The approach is illustrated on exon 1 of human beta-globin gene.

DNA↗
PubMedDate not supplied

On structural interpretation of several distance related topological indices.

We consider the role that individual bonds play in bond-additivities in order to better understand the structural basis of various topological indices. In particular we consider indices closely related to the Wiener index (W) and the distance matrix and search for optimal weights of terminal and interior CC bonds in alkanes for a selection of physicochemical properties. It is interesting to note that different properties are associated with different relative roles of the exterior and the interior CC bonds.

Journal Article↗
PubMedDate not supplied

On use of the variable connectivity index 1chi(f) in QSAR: toxicity of aliphatic ethers.

The number of non-hydrogen atoms in a molecule, N, appears as a very good molecular descriptor for the toxicity of aliphatic ethers, despite the fact that it does not differentiate among isomers. The regression based on N as a descriptor for the toxicity in mice of 21 alkyl ethers was reported to yield the regression coefficient r = 0.9751. The simple connectivity index 1chi produced for the same data a less satisfactory regression: r = 0.9548. To see if variable connectivity index 1chi(f) can improve the regression characterized by N we examined the same data using the variable connectivity index 1chi(f) as a molecular descriptor. By varying x, y, the variables that discriminate between carbon and oxygen atoms, we obtained regression which approaches in quality the best reported regression using weighted paths as descriptor and which is marginally better than the regression based on N.

Journal Article↗
PubMedDate not supplied

A new descriptor for structure-property and structure-activity correlations.

We consider an improvement of a multiple regression analysis (MRA) for the correlation of boiling points of alcohols using descriptors that involve a variable part. In the search for the best descriptors based on weighted paths we came upon a novel molecular descriptor, the use of which was apparently overlooked in the past. The novel descriptor counts paths of length three; however, only those associated with an oxygen atom are counted.

Journal Article↗