A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF

Abstract

We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer–small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF–TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein–protein interactions.

Network pharmacology and experimental verification based research into the effect and mechanism of Aucklandiae Radix–Amomi Fructus against gastric cancer

“…The resolution of the crystal structures to achieve and carry out molecular modeling is 2.5–3.0 A. The PDB IDs corresponding to the hub target proteins selected in this study are AKT1 (PDB ID: 1UNQ 33 ), MAPK3 (PDB ID: 6GES 34 ), IL6 (PDB ID: 4O9H To be published ), MAPK1 (PDB ID: 6OPH 35 ), EGFR (PDB ID: 7JXP To be published ), SRC (PDB ID: 6E6E 36 ), TNF (PDB ID: 7KPA 37 ), CXCL8 (PDB ID: 6WZM 38 ), CASP3 (PDB ID: 6X8K To be published ), and APP (PDB ID: 6ITU 39 ). The SDF files of the main compounds with high degree were downloaded from the PubChem database ( https://www.ncbi.nlm.nih.gov/pccompound/ ) as candidate docking medicinal ingredients, and the docking simulation calculation of molecules and target proteins was carried out by the molecular docking software AutoDock Vina 1.5.6 40 .…”

TNF-α: The shape of small molecules to come?

“…The UCB group developed a conformational selective mAb able to sense the presence of small molecules bound to sTNF-a in complex biological samples. 16 This could become an important tool as an engagement biomarker in future clinical studies, and could also speed up trials and help prove correlations of target engagement with efficacy.…”

Membrane Hormone Receptors and Their Signaling Pathways as Targets for Endocrine Disruptors

“…Concerning TNF signaling, large-scale networks of TNFR trimers must form from pre-ligand assembled dimers for stimulation. Small organic molecules can bias the ensemble of TNFR1 conformational states toward those states associated with activation [ 33 , 34 , 35 ]. A small-size activator of TNFR1 signaling, named SB 200646 hydrochloride (SBH), has been identified and indicates that small hydrophobic molecules should be able to, intentionally or not, play a similar role.…”