The Discovery of Indole-2-carboxylic Acid Derivatives as Novel HIV-1 Integrase Strand Transfer Inhibitors

Abstract

As an important antiviral target, HIV-1 integrase plays a key role in the viral life cycle, and five integrase strand transfer inhibitors (INSTIs) have been approved for the treatment of HIV-1 infections so far. However, similar to other clinically used antiviral drugs, resistance-causing mutations have appeared, which have impaired the efficacy of INSTIs. In the current study, to identify novel integrase inhibitors, a set of molecular docking-based virtual screenings were performed, and indole-2-carboxylic acid was developed as a potent INSTI scaffold. Indole-2-carboxylic acid derivative 3 was proved to effectively inhibit the strand transfer of HIV-1 integrase, and binding conformation analysis showed that the indole core and C2 carboxyl group obviously chelated the two Mg²⁺ ions within the active site of integrase. Further structural optimizations on compound 3 provided the derivative 20a, which markedly increased the integrase inhibitory effect, with an IC₅₀ value of 0.13 μM. Binding mode analysis revealed that the introduction of a long branch on C3 of the indole core improved the interaction with the hydrophobic cavity near the active site of integrase, indicating that indole-2-carboxylic acid is a promising scaffold for the development of integrase inhibitors.

Keywords: HIV-1 integrase; design and synthesis; indole-2-carboxylic acid; structural optimization; virtual screening.

Figure 1

Structure of HIV-1 integrase antagonists and design strategy of new integrase inhibitors. The metal chelating heteroatoms and halogenated phenyl groups interacting with dC20 are colored in red and blue, respectively.

Figure 2

Structure of 10 compounds (1–10) chelating with the magnesium ions of HIV-1 integrase. The metal chelating heteroatoms are in red, and phenyl groups interacting with dC20 are shown in blue.

Figure 3

Binding modes of compounds 4 (A) and 3 (B) with HIV-1 integrase (PDB ID: 6PUY). HIV-1 integrase is displayed in cyan, the 3′ end of the viral DNA (dA21 and dC20) is shown in stick representation in orange, and the chelate bond is represented with dashed line in black.

Figure 4

Optimization strategies of compound 3.

Scheme 1

Synthetic route of compound 3 derivatives. Reagents and conditions: (a) concentrated H₂SO₄, EtOH, 80 °C, 2 h, 65%; (b) POCl₃, DMF, rt-50 °C, 4 h, 87%; (c) Al(O-i-Pr)₃, i-PrOH, 60 °C, 5 h, 85%; (d) p-(trifluoromethyl)benzyl alcohol or o-fluorobenzyl alcohol, K₂CO₃, DMF, rt, 3–5 h, 89–93%; (e) Pd(OAc)₂, Cs₂CO₃, Xphos, 1,4-dioxane, 100 °C, 2–4 h, 68–85%; (f) NaOH, MeOH/H₂O (3:1 v/v), 80 °C, 1.5 h, 45–52%.

Figure 5

Binding modes of compounds 17b (A), 20a (B) and 20b (C) with HIV-1 integrase. HIV-1 integrase is displayed in cyan, the 3′ end of the viral DNA (dC20) is shown in stick representation in orange, and the chelate bond is represented with dashed line in black. dA21 and all water molecules are omitted for clarity.