Computational design of penicillin acylase variants with improved kinetic selectivity for the enzymatic synthesis of cefazolin

Abstract

Enzymatic synthesis plays a pivotal role in the sustainable production of semi-synthetic β-lactam antibiotics. However, these types of green syntheses are being developed slowly because of a lack of appropriate enzymes. In the present work, a computational strategy was developed to identify variants of penicillin G acylase that can catalyze the condensation between methyl 1H-tetrazol-1-yl acetate (TZAM) and 7-amino-3-[(5-methyl-1,3,4-thiadiazol-2-yl) thiomethyl] cephalosphoranic acid (7-ZACA) to produce cefazolin in a fully aqueous medium. An initial library containing 770 sequences was generated by our computational enzyme design program PRODA, which applied a deterministic global minimization algorithm to optimize the binding between the acyl donor and the attacking nucleophile for high kinetic selectivity. The 13 top-ranked variants were subjected to experimental testing based on evaluation by multiple short-time molecular dynamics simulations. A single variant (R145αG) was experimentally confirmed to afford higher kinetic selectivity with a synthesis/hydrolysis ratio (S/H) that was increased by approximately 40% compared with the wild type, and the immobilized enzyme catalyst gave a yield of cefazolin of up to 92% with a 1.8:1 molar ratio of TZAM/7-ZACA, which to our knowledge is the lowest molar ratio of TZAM/7-ZACA to produce a yield over 90%. This study represents considerable progress toward cefazolin synthesis under practical conditions and indicates that this computational strategy could improve enzyme properties for the bio-manufacturing of non-natural molecules.