Molecular Recognition of Macrocyclic Peptidomimetic Inhibitors by HIV-1 Protease^,

Abstract

High-resolution crystal structures are described for seven macrocycles complexed with HIV-1 protease (HIVPR). The macrocycles possess two amides and an aromatic group within 15-17 membered rings designed to replace N- or C-terminal tripeptides from peptidic inhibitors of HIVPR. Appended to each macrocycle is a transition state isostere and either an acyclic peptide, nonpeptide, or another macrocycle. These cyclic analogues are potent inhibitors of HIVPR, and the crystal structures show them to be structural mimics of acyclic peptides, binding in the active site of HIVPR via the same interactions. Each macrocycle is restrained to adopt a beta-strand conformation which is preorganized for protease binding. An unusual feature of the binding of C-terminal macrocyclic inhibitors is the interaction between a positively charged secondary amine and a catalytic aspartate of HIVPR. A bicyclic inhibitor binds similarly through its secondary amine that lies between its component N-terminal and C-terminal macrocycles. In contrast, the corresponding tertiary amine of the N-terminal macrocycles does not interact with the catalytic aspartates. The amine-aspartate interaction induces a 1.5 A N-terminal translation of the inhibitors in the active site and is accompanied by weakened interactions with a water molecule that bridges the ligand to the enzyme, as well as static disorder in enzyme flap residues. This flexibility may facilitate peptide cleavage and product dissociation during catalysis. Proteases [Aba67,95]HIVPR and [Lys7,Ile33,Aba67,95]HIVPR used in this work were shown to have very similar crystal structures.

Mechanism of Substrate Recognition by Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variants Revealed by a Novel Structural Intermediate

“…This is consistent with results obtained from NMR studies (12,16), and therefore a discrete structural intermediate in substrate recognition by HIV-1 protease has been trapped. Both of the flaps in the dimer could potentially assume an intermediate geometry within this crystal form; however, only the flap interacting with the P4-P1 side of the substrate adopts a closed conformation, implying that the P3-P1 region of the substrate may be crucial for specificity (1,27,42). The crystal structure of HIV-1 protease product complex retains only the P5-P1 side (Ac-Ser-Leu-Asn-Phe/) of the substrate Ac-SerLeu-Asn-Phe*Phe-Leu-Glu-Lys (PDB code 1YTH) (43).…”

Viability of a Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variant: Structural Insights for Better Antiviral Therapy

“…In fact, the positions corresponding to the P3-P1Ј sites of the substrates may be used to model inhibitors instead of using the positions of P2-P2Ј. A recent study has revealed that inhibitors with a macrocyclic group connecting the P3 and P1 residues are likely to be more efficient (35).…”

Anisotropic Dynamics of the JE-2147−HIV Protease Complex: Drug Resistance and Thermodynamic Binding Mode Examined in a 1.09 Å Structure,

“…In the case of macrocyclic peptidomimetics, tighter packing of the active site loops of HIV Pr has been correlated with increased binding affinity (41). Clustering of the protein on the basis of ADP interaction profiles indicates that the flaps of monomer A and B and the P1′ binding loop exhibit similar anisotropic motions possibly due to interactions among the flaps.…”