Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted docking

Abstract

BackgroundPreviously, ways to adapt docking programs that were developed for modelling inhibitor-receptor interaction have been explored. Two main issues were discussed. First, when trying to model catalysis a reaction intermediate of the substrate is expected to provide more valid information than the ground state of the substrate. Second, the incorporation of protein flexibility is essential for reliable predictions.ResultsHere we present a predictive and robust method to model substrate specificity and enantioselectivity of lipases and esterases that uses reaction intermediates and incorporates protein flexibility. Substrate-imprinted docking starts with covalent docking of reaction intermediates, followed by geometry optimisation of the resulting enzyme-substrate complex. After a second round of docking the same substrate into the geometry-optimised structures, productive poses are identified by geometric filter criteria and ranked by their docking scores. Substrate-imprinted docking was applied in order to model (i) enantioselectivity of Candida antarctica lipase B and a W104A mutant, (ii) enantioselectivity and substrate specificity of Candida rugosa lipase and Burkholderia cepacia lipase, and (iii) substrate specificity of an acetyl- and a butyrylcholine esterase toward the substrates acetyl- and butyrylcholine.ConclusionThe experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand), although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria.

Prediction of the enantioselectivity of lipases and esterases by molecular docking method with modified force field parameters

“…This result has been widely supported by various previous studies (Hermann et al, 2006;Juhl et al, 2009;Tyagi and Pleiss, 2006). Detailed comparison between GS model and TI model and related discussion was described in the Supplementary Materials.…”

“…However, docking program treats enzyme as static, rigid molecule, so it could not accurately predict the enantioselectivity in all cases. This principal difficulty has been well documented in other studies (Lin et al, 2002;McCammon, 2005) and numbers of potential salvations have been proposed, such as the ''relaxed complex docking'' (Lin et al, 2002) and ''imprinted docking'' (Juhl et al, 2009) method. The MD combined with docking is expected to eliminate this bias.…”

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

“…For these reasons, functional annotation can benefit significantly from structural information, in addition to bioinformatics analysis of protein sequences, as also shown elsewhere (15)(16)(17). By constructing homology models and docking dipeptide substrates, we were able to generate specific hypotheses regarding substrate specificities.…”

A Novel Cold Active Esterase from a Deep Sea Sponge Stelletta normani Metagenomic Library

“…Similar types of molecular docking studies have previously been employed to predict the enantioselectivity of various lipases (Juhl et al, 2009;Ji et al, 2012) and for the substrate specificity of feruloyl esterases (Gupta Udatha et al, 2012). Esterase 7N9 was found to have subtle differences in its CAP and catalytic domain when compared to E40 esterase.…”