Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid

Abstract

Boronic acids have been typecast as moieties for covalent complexation and are employed only rarely as agents for non-covalent recognition. By exploiting the profuse ability of a boronic acid group to form hydrogen bonds, we have developed an inhibitor of HIV-1 protease with extraordinary affinity. Specifically, we find that replacing an aniline moiety in darunavir with a phenylboronic acid leads to 20-fold greater affinity for the protease. X-ray crystallography demonstrates that the boronic acid group participates in three hydrogen bonds, more than the amino group of darunavir or any other analog. Importantly, the boronic acid maintains its hydrogen bonds and its affinity for the drug-resistant D30N variant of HIV-1 protease. The BOH···OC hydrogen bonds between the boronic acid hydroxy group and Asp30 (or Asn30) of the protease are short ( r_O···O = 2.2 Å), and density functional theory analysis reveals a high degree of covalency. These data highlight the utility of boronic acids as versatile functional groups in the design of small-molecule ligands.

Figure 1.

Interactions with a substrate, darunavir, or its analogs and the S2′ subsite of HIV-1 protease. (A) A substrate (PDB entry 1kj7). (B) Darunavir (4hla). (C) Anisole analog (2i4u). (D) Benzyl alcohol analog (3o9g). (E) Cyclopropyl-amino-benzothiazole analog (5tyr). (F) Benzamide analog (4i8z). (G) Boronic acid 1 bound to wild-type HIV-1 protease (6c8x). (H) Boronic acid 1 bound to D30N HIV-1 protease (6c8y). Major conformers are shown for inhibitors that bound in non-symmetry–related conformations.

Figure 2.

Orbital interactions in a model of boronic acid 1 and residue 30 of HIV-1 protease derived from X-ray crystal structures (PDB entries 6c8x and 6c8y). NBO rendering of the hydrogen bond between a boronic acid hydroxy group and O^δ of Asp30 (A) and Asn30 (B) with hydrogen atoms optimized at the M06–2X/6–311+G(d,p) level of theory employing the IEFPCM solvation model.