A COMBINED QUANTUM CLASSICAL MOLECULAR-DYNAMICS STUDY OF THE CATALYTIC MECHANISM OF HIV PROTEASE/

Based on available three-dimensional structures of enzyme-inhibitor co mplexes, the mechanism of the reaction catalysed by HIV protease is st udied using molecular dynamics simulations with molecular mechanics an d combined quantum-mechanics/molecular-mechanics potential energy func tions. The results support the general acid/general base catalysis mec hanism, with Asp25' protonated in the enzyme-substrate complex. In the enzyme-substrate complex, the lyric water molecule binds at a positio n different from the positions of the hydroxyl groups in various aspar tic protease-inhibitor complexes. The carboxyl groups at the active si te also adopt a different orientation. However, when the lytic water m olecule approaches the scissile peptide, the reaction centre changes g radually to a conformation close to that derived from X-ray diffractio n studies of various enzyme-inhibitor complexes. The proton transfer p rocesses can take place only after the lyric water molecule has approa ched the scissile peptide bond to a certain degree. Qualitatively, the free-energy barrier associated with the nucleophilic attack step, whi ch takes place at physiological pH, is comparable with the acid or bas e-catalysed reactions of model systems. The structure of the tetrahedr al intermediate resulting from the nucleophilic attack step also indic ates a straightforward pathway of the next reaction step, i.e. the bre aking of the C-N bond. (C) 1996 Academic Press Limited.