| Regional Biophysics Meeting 2005, March 16-20, Zreče, Slovenia | [ComputModel] |
Enzymes are important molecules for drug design and biocatalysis. In order to study their affinity and specificity we are, besides using the established force field and quantum mechanical methods developing simple, physically based approaches to quantify the relationships between the structural variables and enzyme activity. Starting from the experimental, mostly crystal, structures we model protein mutants and their complexes with substrates and inhibitors. Molecular modelling enables us to track possible binding modes and the conformational changes that occur during binding and to study reactions in an enzyme active site. Further more, we correlate the molecular modelling results with the experimental, kinetic and thermodynamic data and build a QSAR (Quantitative Structure Activity Relationship) model. The QSAR model enables us to predict enzyme selectivity and/or affinity for new compounds, but also to suggest enzyme mutations that will improve its activity. In order to demonstrate such an approach, I will present our study on Burholderia cepacia lipase (BCL) stereoselectivity. We have selected BCL for our study since it is known as useful biocatalyst for obtaining enantiomericaly pure compounds, in particular primary and secondary alcohols and their esters. We used force field and quantum mechanical methods, to model BCL complexes with its inhibitors and esters of primary and secondary alcohols and to investigate the proton transfer reactions in the BCL active site. By the QSAR model developed for secondary aryl-alcohols we were able to unambiguously predict the fast-reacting enantiomer, magnitude of the enantioselectivity and to identify interactions between the substrate and the lipase amino acid residues that play key roles in secondary alcohol enantiodifferentiation. From the results, it was possible to propose modifications of both, substrate and protein, which would directionally modify enantioselectivity of BCL related compounds.
Email: sanja.tomic@irb.hr
Address: Sanja Tomić, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia