Graph Transformation for Enzymatic Mechanisms
| Autor: | Andersen, Jakob L., Fagerberg, Rolf, Flamm, Christoph, Fontana, Walter, Kolčák, Juraj, Laurent, Christophe V. F. P., Merkle, Daniel, Nøjaard, Nikolai |
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| Rok vydání: | 2021 |
| Předmět: | |
| Druh dokumentu: | Working Paper |
| Popis: | Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this complex problem are computationally assisted, the drafting of catalytic mechanisms, i.e. the specification of the chemical steps-and hence intermediate states-that the enzyme is meant to implement, is largely left to human expertise. The ability to capture specific chemistries of multi-step catalysis in a fashion that enables its computational construction and design is therefore highly desirable and would equally impact the elucidation of existing enzymatic reactions whose mechanisms are unknown. Results: We use the mathematical framework of graph transformation to express the distinction between rules and reactions in chemistry. We derive about 1000 rules for amino acid side chain chemistry from the M-CSA database, a curated repository of enzymatic mechanisms. Using graph transformation we are able to propose hundreds of hypothetical catalytic mechanisms for a large number of unrelated reactions in the Rhea database. We analyze these mechanisms to find that they combine in chemically sound fashion individual steps from a variety of known multi-step mechanisms, showing that plausible novel mechanisms for catalysis can be constructed computationally. Comment: Preprint submitted to ISMB/ECCB 2021. Prototype implementation source code available at https://github.com/Nojgaard/mechsearch Live demo available at https://cheminf.imada.sdu.dk/mechsearch/ Supplementary material available at https://cheminf.imada.sdu.dk/preprints/ECCB-2021 |
| Databáze: | arXiv |
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