Biodegradation Prediction Tools

Abstract

Experimental approaches for determining the environmental fate of new molecules generated by the modern chemical and pharmaceutical industry cannot cope with the pace at which new of these substances are synthesized, thus raising questions on their ultimate fate if released into the environment. This has fostered the development of different web-based and publicly available platforms that deliver an appraisal of the amenability of given chemical species to microbial biodegradation. One major class of such predictors foretell the final destiny of an input chemical formula, either as an end-point state (i.e., degradable or not) or as an estimation of half-life under certain circumstances. These tools are characteristically automated and thus most suitable for screening large collections of compounds without any expert knowledge. A second type of platforms provides information on the possible – often alternative – biodegradation routes that the compounds under examination may go through, with an indication of possible intermediates and enzymatic reactions. Such pathway-based tools require a degree of interactivity by the user and are more suited to analyses of individual target molecules. The protocols detailed below describe the practical usage of one platform of each type, specifically, EAWAG-PPS (formerly UM-PPS) and BiodegPred. Both take as an input the formulas of the compounds, but they deliver different and somewhat complementary information on their most likely environmental fate.