Development of Orally Efficacious Allosteric Inhibitors of TNFα via Fragment-Based Drug Design

Abstract

Tumor necrosis factor α (TNFα) is a soluble cytokine that is directly involved in systemic inflammation through the regulation of the intracellular NF-κB and MAPK signaling pathways. The development of biologic drugs that inhibit TNFα has led to improved clinical outcomes for patients with rheumatoid arthritis and other chronic autoimmune diseases; however, TNFα has proven to be difficult to drug with small molecules. Herein, we present a two-phase, fragment-based drug discovery (FBDD) effort in which we first identified isoquinoline fragments that disrupt TNFα ligand–receptor binding through an allosteric desymmetrization mechanism as observed in high-resolution crystal structures. The second phase of discovery focused on the de novo design and optimization of fragments with improved binding efficiency and drug-like properties. The 3-indolinone-based lead presented here displays oral, in vivo efficacy in a mouse glucose-6-phosphate isomerase (GPI)-induced paw swelling model comparable to that seen with a TNFα antibody.

In Silico Identification and Evaluation of Natural Products as Potential Tumor Necrosis Factor Function Inhibitors Using Advanced Enalos Asclepios KNIME Nodes

“…TNF has been broadly studied and reviewed in the literature [ 7 , 8 , 9 , 10 , 11 , 12 , 13 ], underlining the importance and the relevance of this growth factor as a valuable drug target.…”

“…All interactions were hydrophobic, while interactions of the ligand with TNF residues Tyr59 and Tyr119 were identified as highly important for TNF inhibition [ 5 ]. Starting from the ligand SPD304 in 2005, several small molecule TNF inhibitors have been developed, including heterocyclic compounds, small organic ligands, natural products (NPs) and metal-complexed compounds [ 10 , 11 , 12 , 26 , 27 , 28 ]. Blevitt et al [ 29 ] discovered an inhibitor that forms an aggregating conglomerate, which antagonizes a protein subunit of the TNF trimer and alternates the quaternary structure of TNF upon binding.…”

“…Thus, the formation of the TNF-TNFR1 is disrupted, due to the quaternary structure change induced by the aggregate. O’Connell et al [ 27 ] and Dietrich et al [ 12 ] developed small molecules with oral bioavailability that bind deeply in the TNF homotrimer, being able to allosterically stabilize an asymmetric complex or the trimer itself, leading to signaling inhibition. Xiao et al [ 30 ] also proposed a compound that deforms the TNF trimer upon binding, leading to deregulated signaling upon binding of the TNF trimer to TNFR1.…”

Unexpected Similarity Between HIV‐1 Reverse Transcriptase and Tumor Necrosis Factor Binding Sites Revealed by Computer Vision.

“…In absence of X-ray structures of TNF-α bound to efavirenz and delavirdine, we cannot rule out the possibility that both inhibitors bind to a different pocket than that highlighted in the current computational study. This hypothesis is however very unlikely for two reasons: (i) no other cavity than that occurring at the inner core of the multimeric TNF-α could be detected among the currently existing 33 structures available in the Protein Data Bank; (ii) all non-covalent small molecular weight inhibitors co-crystallized with TNF-α dimeric or trimeric forms [32][33][34][35] are exactly bound at the central pocket examined in this study.…”

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

“…Recently, scientists from Abbvie and Bristol Myers Squibb (BMS) disclosed the discovery of potent orally bioavailable molecules (3 and 4) displaying in vivo efficacy in animal models of inflammation comparable to a TNF-a antibody. 14,15 The Abbvie group described a two-phase approach, including a nuclear magnetic resonance (NMR)-based fragment-based drug discovery (FBDD) effort leading to the discovery of the isoquinoline core 5 disrupting the protein-protein interactions (PPIs) through allosteric desymmetrization of TNF-a observed from highresolution crystal structures (Fig. 3).…”