CONFORMATIONAL-ANALYSIS OF HIV-1 PROTEASE INHIBITORS .2. THIOPROLINE P'(1) RESIDUE IN THE POTENT INHIBITOR KNI-272

The very potent HIV-1 protease (HIV-PR) inhibitor, KNI-272, contains a norstatine-thioproline linkage at P-1-P-1'. The three-dimensional cry stal structure of this compound bound to HIV-PR has recently been dete rmined [Baldwin et al., Structure, 3, 581 (1995)]. The crystal structu re reveals a number of interesting interactions previously unseen in b ound HIV-PR inhibitors. Here, we employ high-level ab initio calculati ons and molecular modeling to ascertain the strain energy of the bound conformation of the norstatine-thioproline portion of KNI-272. Baldwi n et al. suggested that two of the reasons for the high potency of KNI -272 are the rigidity of its backbone and a strong preference for the norstatine-thioproline amide linkage to adopt a trans conformation. Ou r analysis shows that, on the contrary, there is still considerable fl exibility in the backbone of the norstatine-based inhibitor. Furthermo re, in the gas phase and in solution, there are both cis and trans con formations of the norstatine-thioproline amide linkage which are low i n energy. However, when bound in the active site of HIV-PR, KNI-272 cl early has a strong preference for a trans conformation, which enables the formation of hydrogen bonds to the flap water. Our calculations, a t level up to MP2/6-31++G*//HF/6-31G*, suggest that the bound, trans amide conformation of the norstatine-thioproline ''core'' is still str ained by 2-3 kcal/mol, primarily due to the placement of the P-1' thio proline carboxamide. This result is consistent with those previously o btained for the related protease inhibitor Ro 31-8959 (Saquinovir), wh ich also requires a carboxamide to adopt a high-energy rotamer to pres erve a good hydrogen bond to the flap water. However, the strain of th e bound conformation of KNI-272 is clearly lower than that of Saquinov ir. In addition, because the norstatine linkage does not contain a bas ic amine (as do Saquinovir and JG-365, for example) it should be easie r to desolvate, which also assists in binding. The relationship betwee n KNI-272, JG-365, Saquinovir, and P-1' proline-containing substrate a lso is discussed. (C) 1997 by John Wiley & Sons, Inc.