EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions

Abstract

A rich literature dedicated to understanding the reaction mechanisms of hundreds of enzymes has emerged over time from the works of experimental and computational researchers. This body of information can now be the starting point for an entirely novel approach to studying enzyme mechanisms using knowledge-based prediction methods. Here, we present such a method, EzMechanism, (pronounced as "Easy Mechanism") which is able to automatically generate mechanism proposals for a given active site. It works by searching the chemical reaction space available to the enzyme using a set of newly created biocatalytic rules based on knowledge from the literature. EzMechanism aims to complement existing methods for studying enzyme mechanisms by facilitating and improving the hypotheses generating step. We show that EzMechanism works by validating it against 56 enzymes with a known mechanism and identify the limited coverage of the current ruleset as the main target for further improvement.