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Biomolecular Computations toward Enzyme-Catalyzed Transformations of Non-Natural Organic Compounds : Ab initio Fragment Molecular Orbital Calculations

Our group had a long standing interest in utilizing biomolecules, such as enzyme proteins and carbohydrates, in the fields of organic synthesis and bioorganic chemistry [1]. Protein lipases are enzymes transforming a variety of non-natural organic compounds including alcohol and ester molecules and are among the most widely used biocatalysts in the synthesis of enantiomerically pure chiral compounds of biological relevance. Although a large amount of experimental data, involving our results [2], is available for two popular lipases, Candida antarctica lipase typeB (CALB) and Pseudomonas cepacia lipase (PCL), the mechanism of their enantioselectivity is still not completely elucidated [3]. Recently we have focused our attention on the computer modeling of lipase enzyme-ligand complexes to understand the enantiopreference and enantioselectivity of lipases toward chiral organic compounds. Molecular dynamics simulations of CALBand PCL-chiral alcohol ester complexes indicated that the C-O distance in each complex between the carbonyl carbon of chiral ester and the oxygen of the active site Ser side chain OH is shorter for the fast reacting (R)-enantiomer than for the slow reacting (S)-enantiomer [4]. It is anticipated that the difference of the C-O distance makes it possible to predict the enantiopreference of CALB toward secondary alcohols. In this presentation we highlight the ab initio fragment molecular orbital (FMO) calculations of CALB complexed with secondary alcohol esters [5]. In addition, we present FMO calculations on the tetrahedral intermediate in the hydrolysis of secondary alcohol esters.