CALCULATION OF RELATIVE DIFFERENCES IN THE BINDING FREE-ENERGIES OF HIV-1 PROTEASE INHIBITORS - A THERMODYNAMIC CYCLE PERTURBATION APPROACH

An iterative computer-assisted drug design (CADD) method that combines molecular mechanics, dynamics, thermodynamic cycle perturbation (TCP) calculations, molecular design, synthesis, and biochemical testing of peptidomimetic inhibitors and crystallographic structure determinatio n of the protein-inhibitor complexes has been successfully applied to the design of novel inhibitors for the HIV1 protease. The first ''desi gner'' compound in this series (I) was designed by replacing the C-ter minal Val-Val methyl ester of a known hydroxyethylene inhibitor with a diphenhydramine amide derivative in which two phenyl groups fill the p2' and p3' side-chain binding pockets in the HIV1 protease. Subsequen t testing showed modest inhibition (K-i = 1.67 mu M). Concurrently, mo lecular mechanics calculations on designed analogs indicated the feasi bility of replacement of a phenyl ring with an indole ring (II). Synth esis and biochemical testing resulted in better inhibition potency for II. X-ray crystal structure determination of HIV1 protease complexed with I and II provided structural information for subsequent design an d TCP calculations. A TCP protocol was established and validated for t he mutation of I --> II. TCP results showed a net gain of 2.1 (+/-0.9) kcal/mol in replacing II with I, which agreed with experimental resul t within an error margin-of 0.8 kcal/mol. TCP calculations for six oth er mutations (I --> III, II --> III, IV, V, VI, and VII) were performe d prior to synthesis and testing. These results allowed for the priori tization of design ideas for synthesis. In all cases where experimenta l results are available, TCP calculations showed good agreement. These results demonstrate that the TCP approach can be used with medicinal chemistry and crystallography for screening the proposed derivatives o f a lead compound prior to synthesis, thus potentially reducing the ti me for the discovery of new drugs.