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 noncovalent 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, exceeding that of 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 (rO⋯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.

Potent HIV‐1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein‐Ligand X‐ray Structural Studies

“…[35] Interestingly,i nt his cell-based antiviral assay,i nhibitor 3 did not exhibit appreciable antiviral activity with IC 50 values of 1 mm and 1mm,i nM T-2a nd MT-4 cells, respectively.C arboxamided erivative 4 showed very potent enzyme K i anda ntiviral IC 50 values of 93 nm and 38 nm in MT-2 and MT-4 cells, respectively.B oth carboxylic acid containing inhibitors 11 and 13 showede xcellent enzyme inhibitory activity (K i 7.6 and 3.2 pm,r espectively) however,t hey did not show antiviral activity.B oronic acid derivative 5 has been shown to have very potent enzyme inhibitory activity of 0.5 pm. [26] However,t here is no report of its antiviral activity in ac ell-based assay.W eh ave evaluated the boronic acid PI 5 in an antiviral assay with MT-2 cells. It turned out that boronic acid derivative 5 showedi mproved antiviral IC 50 value of 48.9 nm compared to carboxylic derivatives 3 and 4 (entry 2, Ta ble 1).…”

Boronic Acids and Their Derivatives in Medicinal Chemistry: Synthesis and Biological Applications

“…The HIV-1 protease is also critical in viral replication, so inhibitors of this enzyme are a good approach for developing HIV antiviral drugs. The drug darunavir is known to be a HIV-1 protease inhibitor and its mechanism of action consists in targeting the S2′ enzymatic subsite, forming hydrogen bonds with the amides present in Asp30 [ 72 , 73 ]. An ideal protease inhibitor must have the ability to interact with three local sides; these include the main chain and side chain of Asp30 and a molecule of water coordinated to the main chain of Gly48.…”

“…An ideal protease inhibitor must have the ability to interact with three local sides; these include the main chain and side chain of Asp30 and a molecule of water coordinated to the main chain of Gly48. Based on the knowledge that boronic acids can form strong hydrogen bonds and these bonds are essential for this inhibitory activity, a 4-sulfonylphenylboronic acid (compound 84 ) was designed through replacement of the 4-sulfonylaniline of darunavir, and the effects of this substitution were analyzed [ 72 ]. It was observed that the boronic acid 84 acts as a competitive inhibitor of HIV-1 protease and that the affinity towards the target was 20-fold greater than darunavir (darunavir, K i of 10 pM; boronic acid derivative 84 , K i of 0.5 pM).…”

“…X-Ray crystallography studies proved that the boronic acid moiety interacts with all three locals referenced above, thus contributing to a significantly better affinity. Besides these proprieties, this boronic acid ( 84 ) is non-toxic to human cells and, unlike aniline moiety in darunavir, has no related genotoxicity as a result of in vivo metabolic activation, since that the product of metabolic phase I activation in boronic acids is an alcohol, later metabolized in phase II in order to be eliminated from the body [ 72 ].…”

“…The initial step corresponds to a coupling reaction between the starting material 82 and 4-bromobenzenesulfonyl chloride, followed by a palladium-coupling reaction with B 2 pin 2 and further addition of 2,5-dioxopyrrolidin-1-yl((3R,3S,6R)-hexahydrofuro[2,3b]furan-3-yl) carbonate. The hydrolysis of intermediate 83 leads to the final product 84 [ 72 ].…”