Thermodynamics-Based Drug Design: Strategies for Inhibiting Protein–Protein Interactions

Abstract

The inhibition of protein–protein interactions and their ensuing signaling processes play an increasingly important role in modern medicine. Small molecular-weight inhibitors that can be administered orally are the preferred approach but efficient strategies for developing them are not yet generally available. Due to the large size difference between the protein–protein interface and the small molecule, inhibitor interactions are expected to extend to only a small region of the interface. If this is the case, classical competitive inhibition may be hard to achieve. In addition, competitive inhibition wastes binding energy that can be effectively used to inhibit signaling. The best and most energy-efficient approach would be the development of small molecules that bind at the protein–protein interface and inhibit the signaling process without displacing the protein ligand. This approach seems feasible knowing that the binding energy is not evenly distributed within the binding interface but concentrated in discrete hotspots, and that the initiation of signaling may not overlap with those hotspots. We outline a general protein–protein inhibition model that extends from competitive to noncompetitive scenarios and apply it to the development of HIV-1 gp120-CD4 inhibitors. This rigorous model can be easily applied to the analysis of protein–protein inhibition data and used as a tool in the optimization of inhibitor molecules.

An Innovative High-Throughput Screening Approach for Discovery of Small Molecules That Inhibit TNF Receptors

“…7 Triclabendazole’s relative potency, which bears future investigation, is therefore consistent with the notion that non-competitive inhibitors that alter conformationally active regions of proteins should be more potent. 32 …”

“…In general, small-molecule inhibitors that do not directly compete with protein-protein interactions may be the most effective for the simple fact that they are unencumbered by competition. 32–34 In the specific case of triclabendazole, we can safely assume that the binding of the small molecule is to either the ECD or TM domain of TNFR1, because the intracellular domains in our FRET constructs are replaced with fluorescent tags, which were shown to have no interaction with the small-molecule compounds (Figure S1B). Therefore, triclabendazole may act allosterically to disrupt receptor oligomerization; or, based on more recent discussions of small-molecule strategies for targeting receptor-receptor interactions, 32,34 it may bind to conformationally active sites of the receptor and disrupt the propagation of the downstream signaling.…”

Identification of the functional binding pocket for compounds targeting small-conductance Ca2+-activated potassium channels

“…Typically, the protein-protein interface is fairly large (~700–4000 Å 2 ), and the size differences make it impossible for small molecules to completely block the protein-protein interactions like the traditional agonists/antagonists. Within the protein-protein interface, smaller regions, or “hotspots”, are responsible for a disproportionate contribution to the binding energy of the two interacting proteins and are targets for theraputics 44–45 . Our structure data show that the binding pocket for PHU and 1-EBIO includes L480 (Figs.…”

Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-ray and Thermodynamic Characterization

“…This strategy implies improving binding affinity ( ΔG ), while simultaneously minimizing the unfavorable binding entropy. 23 The optimization strategy essentially combines standard SAR with thermodynamic analysis by Isothermal Titration Calorimetry (ITC). Importantly, thermodynamic-guided alanine scanning mutagenesis has recently demonstrated that gp120 residue contributions to allosteric structuring are not proportional to binding affinity, providing a structural foundation to the finding that not all NBD-like compounds elicit the unwanted allosteric structuring.…”