Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases using in Silico Screening
| Authors | |
|---|---|
| Year of publication | 2015 |
| Type | Article in Periodical |
| Magazine / Source | Journal of Chemical Information and Modeling |
| MU Faculty or unit | |
| Citation | |
| web | http://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2015/01/jcim15.pdf |
| Doi | http://dx.doi.org/10.1021/ci500486y |
| Field | Biochemistry |
| Keywords | in Silico Screening;Haloalkane Dehalogenases |
| Description | The substrate specificity is a key feature of enzymes determining their applicability in biomaterials and biotechnologies. Experimental testing of activities with novel substrates is a time-consuming and inefficient process, typically resulting in many failures. Here, we present an experimentally validated in silico method for the discovery of novel substrates of enzymes with known reaction mechanism. The method was developed for a model system of biotechnologically relevant enzymes, haloalkane dehalogenases. Based on the parameterization of six different haloalkane dehalogenases with 30 halogenated substrates, mechanism-based geometric criteria for reactivity approximation were defined. These criteria were subsequently applied to the previously experimentally uncharacterized haloalkane dehalogenase DmmA. The enzyme was computationally screened against 42,000 compounds, yielding 548 structurally unique compounds as potential substrates. Eight out of sixteen experimentally tested top-ranking compounds were active with DmmA, indicating a 50% success rate for the prediction of substrates. The remaining eight compounds were able to bind to the active site and inhibit enzymatic activity. These results confirmed good applicability of the method for prioritizing active compounds – true substrates and binders – for experimental testing. |
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