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Abstract

We evaluate the applicability of automated molecular docking techniques and quantum mechanical calculations to the construction of a set of structures of enzyme-substrate complexes for use in Comparative binding energy (COMBINE) analysis to obtain 3D structure-activity relationships. The data set studied consists of the complexes of eighteen substrates docked within the active site of haloalkane dehalogenase (DhlA) from Xanthobacter autotrophicus GJ10. The results of the COMBINE analysis are compared with previously reported data obtained for the same dataset from modelled complexes that were based on an experimentally determined structure of the DhlA-dichloroethane complex. The quality of fit and the internal predictive power of the two COMBINE models are comparable, but better external predictions are obtained with the new approach. Both models show a similar composition of the principal components. Small differences in the relative contributions that are assigned to important residues for explaining binding affinity differences can be directly linked to structural differences in the modelled enzyme-substrate complexes: (i) rotation of all substrates in the active site about their longitudinal axis, (ii) repositioning of the ring of epihalohydrines and the halogen substituents of 1,2-dihalopropanes, and (iii) altered conformation of the long-chain molecules (halobutanes and halohexanes). For external validation, both a novel substrate not included in the training series and two different mutant proteins were used. The results obtained can be useful in the future to guide the rational engineering of substrate specificity in DhlA and other related enzymes.

Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26

“…It was assumed that the differences in K m values capture, to a large extent, differences in binding affinities. This concept was proven in the similar analyses conducted for the haloalkane dehalogenase DhlA ( , ). Log K m values were initially correlated with one descriptor at a time using linear regression analysis.…”

“…Comparative binding energy (COMBINE) analysis () is a technique for deriving QSARs from a set of three-dimensional structures of enzyme−ligand complexes. COMBINE analysis was originally applied to enzyme−inhibitor interactions in the drug design field, whereas its applicability to studying enzyme−substrate binding and to protein design has been tested more recently ( − ). Thus, a COMBINE model was constructed for DhlA () that quantitatively accounted for 91% (73% cross-validated) of the variance in the apparent dissociation constants of 18 substrates and identified the residues contributing most significantly to the substrate specificity of this haloalkane dehalogenase.…”

Modulation of Binding Strength in Several Classes of Active Site Inhibitors of Acetylcholinesterase Studied by Comparative Binding Energy Analysis

“…At the end of the procedure, those pairwise interactions between the ligand and individual protein residues that are predictive of activity or binding free energy (i.e., the real “signal”) are selected and given weights, according to their importance in the model, in the form of PLS pseudocoefficients, whereas the “noise” present in the dataset is filtered out. This approach has been termed comparative binding energy (COMBINE) analysis, and, since its first implementation in 1995, several successful applications on different systems of medicinal chemistry − and biochemical − interest have been reported in the literature by a number of laboratories.…”

A Docking Score Function for Estimating Ligand−Protein Interactions: Application to Acetylcholinesterase Inhibition

“…The chosen conformations were used to fit an interaction field whose form, basically a variant of the comparative binding energy (COMBINE) method, − is as follows: where c i and d j are fitted coefficients, and are electrostatic and van der Waals (VDW) interactions arising between atoms in the i th and j th residues and the ligand. In this expression, all receptor residues within 10 Å of the position of the original E2020 ligand (a total of 92 residues) were included in the summation over i , and and were calculated via an SVL script written for the MOE system.…”