Comparative Molecular Field Analysis of Substrates for an Aryl Sulfotransferase Based on Catalytic Mechanism and Protein Homology Modeling

Abstract

Comparative Molecular Field Analysis (CoMFA) methods were used to produce a 3D-QSAR model that correlated the catalytic efficiency of rat hepatic aryl sulfotransferase (AST) IV, expressed as log(k(cat)/K(m)), with the molecular structures of its substrates. A total of 35 substrate molecules were used to construct a CoMFA model that was evaluated on the basis of its leave-one-out cross-validated partial least-squares value (q(2)) and its ability to predict the activity of six additional substrates not used in the training set. The model was constructed using substrate conformations that favored (1) proton abstraction by the catalytic histidine residue, (2) an in-line sulfuryl-group transfer mechanism, and (3) constraints imposed by the residues lining the substrate binding pocket of a homology model of AST IV. This CoMFA model had a q(2) value of 0.691, and it successfully predicted the activities of the six molecules not used in the training set. A final CoMFA model was constructed using the same methodology but with molecules from both the training set and the test set. Its q(2) value was 0.701, and it had a non-cross-validated r(2) value of 0.922. The contour coefficient map generated by this CoMFA was overlaid on the amino acids in the substrate-binding pocket of the homology model of AST IV and found to show a good fit. Additionally external validation was obtained by using the CoMFA model to design substrates that show high activities. These results establish a methodology for prediction of the substrate specificity of this sulfotransferase based on CoMFA methods that are guided by both the homology model and the catalytic mechanism of the enzyme.

Accurate Prediction of Glucuronidation of Structurally Diverse Phenolics by Human UGT1A9 Using Combined Experimental and In Silico Approaches

“…As stated by Sharma and Duffel (42,43), in the case of enzymes that may exhibit nonproductive binding interactions with some substrates, a highly relevant kinetic parameter for a CoMFA correlation of the structure to its ability to serve as a substrate for such enzymes is the CL int value, or log (CL int ). This is because CL int is independent of nonproductive binding contributions.…”

Sub- and Supercritical Chiral Separation of Racemic Compounds on Columns with Stationary Phases Having Different Functional Groups

“…Their structures are simple, and they all contain a benzene ring that allows detection at ultraviolet wavelengths. aTetralol (1) is a chiral secondary alcohol used as a substrate 15) or starting material in enantioselective syntheses. 16,17) 2-Phenylpropionic acid (2) is an acidic compound that possesses a carboxyl group and is used to synthesize optically active compounds, for example, xanthine derivatives 18) and tetrapeptides.…”

From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function

“…The value of sulfotransferase crystal structures has extended beyond basic understanding of the enzymatic functions, serving as a starting point for in silico calculations to predict substrates and inhibitors and better understand how conformational dynamics affect substrate binding. Early work applied crystal structures and homology models to an adaptation of the three-dimensional quantitative activity relationship (QSAR), referred to as comparative molecular field analysis (CoMFA), to better understand enzyme kinetics and help predict specificity of rat ASTIV and SULT1A3 (Sharma and Duffel, 2002;Sipilä et al, 2003). In silico docking based on crystal structures was used to determine that PAPS binding can regulate binding of larger substrates such as Raloxifene via conformational dynamics of loop 3 (Cook et al, 2012).…”