IDENTIFICATION OF NATURAL PRODUCT-DERIVED COMPOUNDS THAT INHIBIT HIV-1 ENTRY INTO TARGET CELLS

ABSTRACT HIV-1 infection is mediated by the interaction between the host cellular CD4 receptor and co-receptors with HIV Envelope protein (Env). Inhibition of HIV entry into host cell presents a biological target for therapeutic intervention. Broadly neutralizing antibody (bNabs) are potent in neutralizing a broad range of HIV strains by binding to the Env and preventing entry into the host cell. VRC01 is a CD4 binding-site class bNabs that binds to the conserved CD4 binding region of Env. However, using antibodies as therapeutic agents pose challenges of low availability and high cost of production. Natural products that can mimic VRC01 bNabs by interacting with the conserved CD4-binding regions may serve as new generation of HIV-1 entry inhibitors, which are broadly reactive and potently neutralizing. This study aimed to identify natural products that mimic VRC01 broadly neutralizing antibody, by interacting with the CD4-bs of HIV-1 gp120 and inhibit viral entry into a target cell. A library of purchasable compounds derived from natural products was virtually screened against the HIV-1 gp120 of clade A/E recombinant 93TH057 (PDB: 3ngb) using AutoDock Vina, and LIGPLOT was used to elucidate the interactions between the compounds and the HIV-1 gp120 complexes. The compounds with the lowest binding energies were selected and further screened against gp120 of a reference HIV strain (HXB2). Pharmacological profiling of the compounds was undertaken using SwissADME. Ten selected compounds were purchased and used for cell-based antiviral infectivity inhibition assay using HXB2-env pseudotype virus. Three compounds, NP-005114, NP-008297 and NP-007382 inhibited entry of HIV HXB2 pseudotype virus into target cells, while the rest of the compounds showed no inhibitory activity against HIV entry into target cells. NP-005114, extracted from the seed of T. chebula, had IC50 of 10μg/ml. Protein-ligand interaction showed that NP-005114 had inter-molecular hydrogen bond interactions with eight and eleven amino acid residues on the CD4-binding site of recombinant clades A/E and B HIV -1 gp120, respectively. NP-005114 had intermolecular hydrogen and hydrophobic interactions with Asp457, a critical amino acid residue in the Phe43 cavity of the HIV gp120 for recombinant clades A/E and B, respectively. Derived from the leaf of Ginkgo biloba, NP-008297 formed ten and four hydrogen bond interactions with amino acid residues of the CD4-binding site on HIV-1 gp120 of recombinant clades A/E and B, respectively. NP-008297 inhibited viral entry at IC50 of 15.5μg/ml. NP-007382 was derived from bacteria and interacted with five amino acid residues in the CD4-binding site of HIV-1 gp120 of recombinant clades A/E and B, via intermolecular hydrogen bond. The 50% inhibitory concentration of NP-007382 against viral entry into the target cell was 13.1μg/ml. These compounds inhibited the entry of HIV clade B pseudotype (HXB2) with an IC50 which was comparable to that of VRC01 (0.1-50 μg/ml) against HIV clade B pseudotypes and primary isolate. The interaction of the compounds with critical residues of the CD4-binding site of more than one clade of HIV-gp120 demonstrates the possibility of broad entry inhibition of other HIV clades. This is the first report of the characterization of NP-008297, NP-00738, and NP-005114 as HIV-1 entry inhibitors.