A novel approach to the use of graph theory in structure-activity relationship studies. Application to the qualitative evaluation of mutagenicity in a series of nonfused ring aromatic compounds

Topological shape and size of peptides: identification of potential allele specific helper T cell antigenic sites

A database of primary sequences of 28 immunogenic peptides, known to elicit T cell response, derived from five different haplotypes was compiled to identify allele specific helper T cell antigenic sites using a rule based graph-theoretical method. The prediction was based on the identification of allele specific patterns in the form of "topological shape and size" present in the peptides. Indices computed from weighted connected graph models of amino acid side chains and peptides were used in this purpose. The system was trained by 10 Ad and 10 non-Ad restricted peptide sequences, assigned actives and inactives, respectively, chosen randomly from the database, and four Ad and four non-Ad restricted sequences were kept as test peptides. This allowed the system to learn about "topological shape and size" specific for Ad restricted peptides from the differences, if any, they had with the inactive peptides in that respect. The system made 100% correct prediction for the training set peptides and misclassified only one inactive peptide of the test set. The system also identified crucial residues for lambda repressor 12-24 and insulin A-chains. This identification also shows that activity related/crucial residues could be located at varying distances from the peptide terminals. To our knowledge, the method is unique of its kind in the literature and may find application in the rational design of synthetic vaccines and other peptides of immunological importance.

Pentachlorophenol

Pentachlorophenol (PCP) is a substance whose widespread use, mainly in wood protection and pulp and paper mills, has led to a substantial environmental contamination. This in turn accounts for a significant exposure of the general human population, with rather high exposure levels being attained in occupational settings. Investigations on the genotoxic activity of PCP have given rise to divergent results which would seem to make an evaluation difficult. By grouping them into 3 categories a somewhat clearer picture, allowing finally an (admittedly tentative) assessment, can be obtained. PCP does seem to be at most a weak inducer of DNA damage: it produces neither DNA-strand breaks nor clear differential toxicity to bacteria in rec-assays in the absence of metabolic activation. Also in SCE induction no increase can be observed in vivo, while PCP is found marginally active in a single in vitro experiment. Metabolic activation, however, leads to prophage induction and to DNA strand breaks in human lymphocytes, presumably through the formation of oxygen radicals. A possible further exception in this area might be the positive results in the yeast recombination tests, although their inadequate reporting makes a full evaluation difficult. PCP does not seem to induce gene (point) mutations, as most bacterial assays, the Drosophila sex-linked recessive lethal test and in vitro assays with mammalian cells did not demonstrate any effects. Marginally positive results were obtained in the mammalian spot test in vivo and in one bacterial test; the positive result in the yeast assay for cycloheximide resistance is fraught somewhat with its questionable genetic basis. PCP does, however, induce chromosomal aberrations in mammalian cells in vitro and in lymphocytes of exposed persons in vivo. Those in vivo results that were unable to provide evidence of chromosomal damage are hampered either by methodological inadequacies or by too low exposure levels. The (rodent) metabolite tetrachlorohydroquinone might be a real genotoxic agent, capable of binding to DNA and producing DNA strand breaks; this activity is probably due to semiquinone radical formation and partly mediated through active oxygen species. Since this compound has not been tested in the common bacterial and mammalian mutagenicity assays, the few ancillary results on this substance cannot be used in a meaningful human risk assessment of PCP. Furthermore, this metabolite has only been produced by human liver microsomes in vitro, but has not been detected in exposed humans in vivo.(ABSTRACT TRUNCATED AT 400 WORDS)