Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures

Abstract

To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercially available compounds. Two of the structures are for WT-virus with different conformations of Tyr181, while the third structure incorporates the Y181C modification. Eventually nine compounds were purchased and assayed. Three of the compounds show low-micromolar antiviral activity toward either or both the wild-type and Y181C HIV-1 strains. The study illustrates a viable protocol to seek anti-HIV agents with enhanced resistance profiles.

Figure 1

Superposition of crystal structures illustrating the alternative orientations of Tyr181 and Tyr188 in the NNRTI binding site. 1rt4 in blue represents a conventional structure for a RT complex, while 2be2 in magenta illustrates the rare alternative with Y181 in the “down” conformation, as found in apo structures such as for 1rtj in white. The ligands in the 1rt4 and 2be2 structures are not shown.

Figure 2

Superimposed NNRTI binding sites and ligands from the three crystal structures. 1rt4 is displayed in blue, 2be2 in magenta, and 1jla in green. Ligand structures are also shown in Scheme 1.

Scheme 1

Ligands in the 1rt4, 1jla, and 2be2 crystal structures.

Figure 3

Comparison of Glide SP poses (in white) and the crystal structures for self-docking the 1jla (left) and 2be2 (right) ligands. RMSD for 1jla is 0.76 Å, and for 2be2 it is 1.03 Å.

Figure 4

The two hierarchical screening protocols used with the three receptors. In the parallel mode, XP scoring was performed on the top 5000 compounds from each SP analysis. In the serial mode, XP scoring was applied to the common 4,684 structures that scored in the top 100,000 in all SP runs.

Figure 5

Many top XP-ranked compounds were not considered for purchase owing to ligand strain stemming from twisted ester and amide linkages or overly short intramolecular contacts. In the serial screen, the illustrated compound ranked first for both the 2be2 and 1jla receptors, and it ranked third for the 1rt4 structure.

Figure 6

The purchased compounds. In the virtual screening, compounds 1 - 5 ranked well for all three receptors, while 6 - 9 ranked highly for individual receptors. All compounds also exhibited acceptable predicted properties (Table 1).

Scheme 2

Structures of known NNRTIs, which were also assayed.

Scheme 3

Aligned structures of 1 and a known 1-nM NNRTI.

Figure 7

Complexes for the active compounds 3 (top), 4 (middle), and 5 (bottom) from docking into the three crystal structures for HIV-RT. 3 has a similar binding mode in all cases, while often the binding modes can differ significantly for different RT structures as for 4 and 5.