Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including anti-tumour and anti-viral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not yet been achieved. The catalytic mechanism of patellamide macrocyclization by PatG macrocyclase domain has been investigated using computational methods. We applied a quantum mechanics/molecular mechanics (QM/MM) methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed here begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 to the substrate leads on to the formation of an acyl-enzyme covalent complex. The leaving group (AYDG) of the substrate is protonated by the substrate’s N-terminus leading to the breakage of the P1-P1’ bond. Finally, the substrate’s N-terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. We found that the formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal.mol-1 and 19.8 kcal.mol-1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.
- catalytic mechanism