CALCULATION OF RELATIVE BINDING FREE-ENERGIES OF PEPTIDIC INHIBITORS TO HIV-1 PROTEASE AND ITS I84V MUTANT

A methodology is presented for calculating relative binding free energ ies of enzyme-inhibitor associations in aqueous solvent. The methodolo gy uses synthesis of semiempirical quantum chemistry to determine the protonation state of important residues in the enzyme active site, mol ecular mechanics to determine the gas-phase energetic contributions to the relative binding free energy, and dielectric continuum solvation to calculate electrostatic hydration contributions. The methodology is then applied to the calculation of the relative binding free energy o f the inhibitors KNI-272, Ro31-8959, L-735,524, and A-77003 to HIV-1 p rotease and its I84V mutant. The calculated relative binding free ener gy is sensitive to the active-site protonation state of the aspartic a cid residues of HIV-1 protease. The protonation state is inhibitor dep endent. Given a particular protonation state, it was found that quanti tatively accurate relative binding free energies could only be achieve d when solvent effects were included. Three categories of binding were found. In the first, the change in binding free energy due to mutatio n is mainly due to the change in enthalpic interactions within the inh ibitor-enzyme complex (Ro31-8959). In the second (L-735,524 and A-7700 3), the change in affinity is caused both by a change in enthalpic int eractions within the enzyme and by a change in the hydration energy of the enzyme and inhibitor-enzyme complexes. In the third case (KNI-272 ), the change in affinity is mainly a solvent effect-it is due to chan ges in hydration of the enzyme only. In all cases, it was found that t he I84V mutant enzyme was more stable than the wild-type enzyme. This alone (without consideration of the inhibitor-enzyme complexes) can qu alitatively explain the reduction in binding affinity due to mutation.