Inhibitor design by wrapping packing defects in HIV-1 proteins

Abstract

Two viral proteins, HIV-1 protease and HIV-1 integrase, have been targeted for inhibitor design to prevent assembly and maturation of HIV-1 virions. The enzymatic mechanism of these proteins involves side-chain groups that serve as general acids or bases. Furthermore, catalytic activity requires that water be removed from the microenvironment surrounding the chemical reaction site or be constrained to serve as an activated nucleophile. Here, we identify previously unrecognized structural features that promote water removal from polar catalytic regions. Packing defects in the form of hydrogen bonds that are insufficiently dehydrated intramolecularly, named ''dehydrons,'' are strategically placed in the structure to induce an anhydrous enzymatic pathway. Dehydrons become electrostatically enhanced and stabilized upon further desolvation. Thus, packing defects act synergistically with the polar active groups to enhance the enzymatic electrostatics. However, because dehydrons are sticky, they constitute targets for inhibitor design. We noticed that inhibitors attach to polar surfaces by further desolvating dehydrons, thus blocking the active sites or the sites involved in harnessing the substrate. The dehydrons are thus required for functional reasons, making them suitable targets. The differences in success when targeting HIV-1 protease, feline immunodeficiency virus protease, and HIV-1 integrase are rationalized in terms of the dehydron distribution, revealing possible improvements in the targeting strategy. Principles of design optimization are proposed to create an inhibitor that can be neutralized only at the expense of the loss of catalytic function. The possibility of using drugs that wrap dehydrons to block proteinprotein associations is also discussed.

Feature-similarity protein classifier as a ligand engineering tool

“…The backbone amide-carbonyl HB is here represented as a thick segment joining the electron-deprived amide proton (open disk) and the carbonyl oxygen (red disk). Thus, the extent of intramolecular wrapping, ρ, by nonpolar "greasy" groups (black balls) becomes central to determine its stability and strength ( [8][9][10][11]. Poorly wrapped hydrogen bonds (dehydrons) are solvent-exposed and become strengthened and stabilized by removal of surrounding water.…”

“…In folds for soluble proteins at least two thirds of the backbone hydrogen bonds are wrapped on average by ρ=26.6±7.5 nonpolar groups ( [8][9][10][11]; for other measures of wrapping see [10]). Dehydrons are here defined as hydrogen bonds whose extent of wrapping lies in the tails of the distribution, i.e.…”

“…Dehydrons have been shown to be markers of protein-ligand association [10][11]. Thus, examination of the 814 non-redundant protein-inhibitor PDB complexes revealed that 488 of them have binding cavities with average hydrophobicity, not significantly higher than the rest of the surface.…”

“…While folds are typically conserved across homologs, packing defects in the form of incompletely packed hydrogen bonds, the so-called dehydrons [8][9][10][11], are often not conserved [8]. Side effects resulting from off-target ligand binding may be then minimized by selectively targeting nonconserved dehydrons that may in effect function as selectivity filters [9].…”

“…Dehydrons are targetable because they constitute sticky sites on the protein surface, with a propensity to become further dehydrated by promoting protein associations [10][11]. The term packing refers to a cluster of nonpolar groups framing an anhydrous microenvironment.…”