Project Research Results
Grantee Research Project Results
BESS, A System For Predicting The Biodegradability Of New CompoundsEPA Grant Number: R826114
Title: BESS, A System For Predicting The Biodegradability Of New Compounds
Investigators: Punch, William F.
Institution: Michigan State University
EPA Project Officer: Karn, Barbara
Project Period: November 1, 1997 through October 31, 2000
Project Amount: $285,063
RFA: Technology for a Sustainable Environment (1997)
Research Category: Pollution Prevention/Sustainable Development
Description:The objective of this work is to further develop a software system called BESS (Biodegradation Evaluation and Simulation System) which can predict the biodegradability of a compound based on the structural features of that compound and the prevailing environmental conditions. Approach:
The approach pursued in the development of BESS is based on the iterative use of plausible enzymatic transformations that are hierarchically organized based on knowledge of microbial physiology and ecology. This organization reduces the potentially large number of enzymatic transformations that could apply to a compound, making the approach computationally feasible. Further, only those enzymatic transformations which are most likely to provide anabolic intermediates or energy to microorganisms and thus have evolved through processes of natural selection are used, further reducing complexity.
We have previously initiated the development of Biodegradation Evaluation and Simulation System (BESS) software that employs a fundamentally different approach to the prediction of whether a given chemical will undergo biodegradation in the environment. The approach is based on the simulated application of plausible enzymatic transformations in an iterative manner. The enzymatic transformations are hierarchically organized, reflecting knowledge about the likelihood of any enzyme being applied. Such an organization reduces the potentially large number of enzymatic transformations that could apply, concentrating instead on those rules which are most likely to provide anabolic intermediates or energy (or some other benefit to microorganisms) and thus have evolved through processes of natural selection. Thus far we have codified rules for a limited number of chemical classes, and have a developed prototype software that is capable of correctly simulating the biodegradation of chemicals for which rules have been entered. A user interface has been developed that permits the user to review the proposed path of degradation step-by-step, modify or enter rules to explore "what if" scenarios, and identify metabolites that may accumulate in the environment. In the proposed research we will (i) expand the number and kinds of enzymatic transformations that are codified; (ii) develop and test a rule hierarchy; and (iii) use genetic algorithms as a tool to "discover" rules which suggest as-of-yet unencoded, or even undiscovered pathways, giving the system a great deal of robustness in dealing with novel compounds.Expected Results:
The accomplishments of the proposed research will be:
(1) Development of a software system (BESS) that can predict whether a specific compound is likely to undergo biodegradation in the environment. BESS would serve at least three functions: (a) the use of BESS would allow biodegradability to be considered early in the product development process; (b) BESS could be used by regulatory agencies to guide decisions regarding proposed regulation and testing; and (c) BESS could be used as a tutorial to teach users what features of chemicals or the environment restrict or promote biodegradation.
(2) A compilation of plausible biodegradation rules which, independent of the BESS, will constitute an important resource for environmental scientists.Publications and Presentations:
Publications have been submitted on this project: View all 3 publications for this projectSupplemental Keywords:
computer science, modeling, biodegradation., RFA, Scientific Discipline, Sustainable Industry/Business, Environmental Chemistry, Sustainable Environment, Technology for Sustainable Environment, Biochemistry, computational simulations, biodegradation evaluation system, decision making, software system, computer science, microorganisms, modeling, enzyme transformations, biotechnology, computer generated alternatives