Prediction of enantioselectivity of lipase catalyzed kinetic resolution using umbrella sampling

• Published in: Journal of biotechnology Vol. 283; pp. 70 - 80
• Main Authors: Mathpati, Ashwini C., Bhanage, Bhalchandra M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 10.10.2018
• Subjects: Alcohols - chemistry; Bacterial Proteins - metabolism; Burkholderia cepacia - enzymology; Candida - enzymology; Catalysis; Enantioselectivity; Esterification; Fungal Proteins - metabolism; Hexanes - chemistry; Kinetic resolution; Kinetics; Lipase; Lipase - chemistry; Lipase - metabolism; Models, Molecular; Molecular dynamics; Molecular Dynamics Simulation; Protein Conformation; Stereoisomerism; umbrella sampling; Molecular dynamics; umbrella sampling; Enantioselectivity; Lipase; Kinetic resolution
• ISSN: 0168-1656; 1873-4863
• DOI: 10.1016/j.jbiotec.2018.07.024

•Molecular dynamics simulation of CRL and BCL in n-hexane.•Initial conformation based on protein-ligand interaction from molecular docking.•Simulation of acylated complex of R and S form of four racemic alcohols•Umbrella sampling to estimate the free energy change along the reaction coordinate.•Umbrella sampling predictions in good agreement with experimental data. Enantiopure intermediates are preferred for drug synthesis in pharmaceutical industry. Lipases are widely used for chiral resolution of optically active compounds based on kinetic resolution. In the kinetic resolution, two enantiomers react with different rates in presence of a chiral catalyst or reagent, resulting in obtaining one enantiomer of great excess compared to other. The enantiomeric ratio (E) is closely related to the free energy difference (ΔΔG) of the activated state of substrate enantiomers. Molecular dynamic (MD) simulations with umbrella sampling technique can be used for estimation of activation free energy change of enantiomers. In this work, lipase-catalyzed transesterification of racemic alcohols with single and double hydroxyl groups have been studied. The umbrella sampling studies have been carried out for Candida rugosa lipase and Burkholderia cepacia lipase in n-hexane. The distance between serine residue in the catalytic triad and the ligand has been considered as a reaction coordinate and various conformations have been selected for MD simulation. The E value has been estimated based on free energy change from umbrella sampling. The estimated E values are in good agreement with experimental data. The work highlights changes in lipase conformation in n-hexane, ligand-protein interaction as well as free energy curve as a function of the reaction coordinate.