Structure-based discovery of natural-product-like TNF-α inhibitors

Abstract

Small but effective: two natural-product-like inhibitors of tumor necrosis factor α (TNF-α; represented in green in the picture) have been identified using structure-based virtual screening. These compounds represent only the third and fourth examples of direct targeting of TNF-α by a small molecule, and display potency comparable to that of the strongest TNF-α inhibitor reported to date.

Figure 1

Chemical structures of small molecule TNF-α inhibitors quinuclidine 1, indoloquinolizidine 2 and SPD304.

Figure 2

Low-energy binding conformations of a) 1, b) 2 and c) SPD304 bound to TNF-α dimer generated by virtual ligand docking. The two subunits of the TNF-α dimer are depicted in ribbon form and are colored in contrasted purple (subunit A) and red (subunit B). The small molecules are depicted as a ball-and-stick model showing carbon (yellow), hydrogen (grey), oxygen (red), nitrogen (blue), and fluoride (green) atoms. Hydrogen bonds are depicted as dotted lines. The binding pocket of the TNF-α dimer is represented as a translucent green surface.

Figure 3

Compound inhibition of TNFR-1 binding to immobilized TNF-α (ELISA). Microtitre plates coated with TNF-α were incubated with TNFR-1 together with 1 or 2 at the indicated concentrations. TNFR-1 binding was detected using anti-TNFR antibody and horseradish peroxidase-conjugated secondary antibody. Approximate IC₅₀ values; 1: 10 μM, 2: 50 μM.

Figure 4

Compound inhibition of cellular TNF-α-induced NF-κB activity. HepG2 cells stably transfected with the NF-κB–luciferase gene were stimulated with TNF-α pre-incubated with the indicated concentrations of 1, 2, or SPD304. Cell lysates were analyzed for luciferase activity to determine the extent of NF-κB inhibition. Approximate IC₅₀ values; 1: 5 μM, 2: >30 μM, SPD304: 3 μM.