Molecular Dynamics Simulations of experimentally-evolved halohydrin dehalogenase enzymes for the synthesis of Lipitor

Abstract

Enzymes are the best catalysts known, they allow increasing the rate of a chemical reaction and do it under mild conditions of pressure, temperature and pH suitable for life. With this awareness, there have been a lot of directed evolution studies for the improvement or modification of enzymes for improved production of products such as pharmaceuticals. These strategies require a lot of work, money and time but enzymes obtained are very active. However, they have the disadvantage of not being rational. Moreover, improved protocols for enzyme design completely based on computations, such as the Inside-Out protocol, can also be performed. These are much cheaper and faster, and have the advantage of allowing the rational design of enzymes, but have the limitation of generating variants whose activity is low compared to the directed evolution-based ones. This work focuses on the enzyme haloalcohol dehalogenase (HheC). This enzyme performs the dehalogenation reaction of toxic compounds but also has the ability to catalyze the reverse reaction. This second reaction is very interesting because it allows the synthesis of a precursor of drugs called atorvastatin (Lipitor). Fox et al conducted a directed evolution experiment for haloalcohol dehalogenase which resulted in a variant with 38 mutations and 4000 times more effective for the mentioned reaction of great importance. The data generated in this experiment, and data from Schallmey and collaborators, who created a more efficient variant of the wild-Miquel Estévez Gay type for the reaction previously discussed only by varying two positions, have served as a basis for understanding which is the effect of the mutations introduced in these proteins along the directed evolution pathway. Thanks to this work, have drawn conclusions of great importance for the future improvement of computational protocols for enzyme design, all using simulations of molecular dynamics (MD), which simulate the generated proteins and their ligands in aqueous medium, and analysing the data generated by computational chemistry tools