3D-QSAR Applied to the Quantitative Prediction of Penicillin G Amidase Selectivity

Abstract

A new approach for predicting the selectivity of penicillin G amidase (PGA) -expressed as k cat / K M -is here described. Regression models were constructed correlating the experimentally determined k cat /K M of a limited number of substrates to molecular descriptors calculated by using methods generally employed in drug discovery for quantitative structure-activity relationship (3D-QSAR methods). Two different methods for the calculation of molecular descriptors have been tested, namely GRIND and Volsurf. The real predictions, made on molecules not used for constructing the models, had an accuracy sufficient for being useful in the experimental practice.Both approaches led to models able to predict substrate selectivity even without modelling the enzyme-substrate complex, whereas the prediction of enantioselectivity was feasible only by combining the GRIND approach with the conformational analysis of the substrates inside the enzymes active site. The present approach represents an actual alternative to screening procedures since it allows one to develop a whole predicting model in a few hours, once a small set of experimental data is made available.

Volsurf computational method applied to the prediction of stability of thermostable enzymes

“…The Volsurf method was originally developed for the prediction of pharmacokinetic properties of drugs. The method has demonstrated impressive performances in the prediction of drug solubility, membrane permeation, intestinal adsorption [7] as well as prediction of enzyme substrate selectivity [8].…”

BioGPS Descriptors for Rational Engineering of Enzyme Promiscuity and Structure Based Bioinformatic Analysis

“…In fact, all enzymes are classified on the basis of their main catalytic activities, although some of them are well known for their promiscuity. As an example, 1GM9 (penicillin G amidase) is also employed in biocatalysis for its ability to catalyze the aminolysis and hydrolysis - although not the synthesis – of phenylacetic acid esters [38] , [39] That experimental evidence is reflected by the localization of 1GM9 within the amidase area but at the interface with the esterase group.…”

Lonza: Biotechnology – A Key Ingredient for Success in the Future

“…Methyl group oxidation heteroaromatic compounds [3] Ethyl group oxidation heteroaromatic compounds [4] Selective oxidation polyols [5,6] Hydroxylation heteroaromatic carboxylic acids [7,8,9,10] stereoselective hydroxylation of unactivated carbons [11,12] Reduction Carbonyl reduction β-oxo esters [13,14] Double bond reduction activated enols [15,16] alkenes b Hydrolysis Acetyl hydrolysis α-aminoacids Penicillin [17,18] Ester hydrolysis α-hydroxy carboxylic acids esters [19] Nitrile partial hydrolysis N-containing heterocyclic cyanides [20][21][22][23]24] Amide hydrolysis N-containing heterocylic 2-carboxamides [21,25,26,27] Amination Transamination N-containing-3-amino heterocycles (asymmetric synthesis) [28] N-containing-3-oxo heterocycles (racemic resolution) [ metagenomics, modeling and quantitative structure-activity relationship (3D-QSAR) [31] and increasing advances in instrumentation which allows extremely high throughput screening protocols to be executed. -the increasing public and government awareness of global warming and the necessity to implement environmentally friendly processes.…”