Design of Potent pan-IAP and Lys-Covalent XIAP Selective Inhibitors Using a Thermodynamics Driven Approach

Abstract

Recently we reported that rapid determination of enthalpy of binding can be achieved for a large number of congeneric agents or in combinatorial libraries fairly efficiently. We show that using a thermodynamic Craig plot can be very useful in dissecting the enthalpy and entropy contribution of different substituents on a common scaffold, in order to design potent, selective, or pan-active compounds. In our implementation, the approach identified a critical Lys residue in the BIR3 domain of XIAP. We report for the first time that it is possible to target such residue covalently to attain potent and selective agents. Preliminary cellular studies in various models of leukemia, multiple myeloma, and pancreatic cancers suggest that the derived agents possess a potentially intriguing pattern of activity, especially for cell lines that are resistant to the pan-IAP antagonist and clinical candidate LCL161.

Covalent Inhibitors of Protein–Protein Interactions Targeting Lysine, Tyrosine, or Histidine Residues

“…31,32 More recently, we have also demonstrated that coupling sulfonyl fluoride benzoic acids on the same amines on a peptide ligand can result in peptides that can covalently target the binding sites of Lys residues. 33 Because these approaches can covalently target a surface amino acid at the binding site, the resulting agents can acquire remarkable potency for the intended target. While reactivity, selectivity, and stability of acrylamides and chloroacetamides in targeting Cys residues have been more extensively studied, similar studies characterizing the introduction of aryl-sulfonyl fluoride 34−36 or aryl-fluoro sulfate 37,38 warheads into binding peptides have not been fully investigated, which is the topic of our studies.…”

N‐locking stabilization of covalent helical peptides: Application to Bfl‐1 antagonists

“…Hence, recent years have witnessed increased efforts in devising novel strategies to design potent and selective PPI antagonists. These included the use of short linear peptides and their subsequent optimizations using structure‐based approaches, and recent examples suggest that the derivation and optimization of short linear peptides into potent, cell permeable, pharmacologically active agents are possible (Baggio et al, ; Baggio, Udompholkul, Barile, & Pellecchia, ). Nonetheless, improving potency, selectivity, and overall drug likeness (i.e., cell permeability) of these agents remain a major challenge.…”

“…Nonetheless, improving potency, selectivity, and overall drug likeness (i.e., cell permeability) of these agents remain a major challenge. More recently, introduction of covalent warheads on peptide or peptide mimetics to target Cys (de Araujo, Lim, Good, Skerlj, & Fairlie, ; Baggio et al, ; Barile et al, ; Harvey et al, ; Huhn, Guerra, Harvey, Bird, & Walensky, ; Stebbins et al, ), and more recently also Lys and Tyr residues (Baggio et al, ), is emerging strategies to increase affinity and selectivity of these agents. A large number of therapeutically viable PPIs are mediated by an alpha helix (Bullock, Jochim, & Arora, ; Sawyer, Watkins, & Arora, ), suggesting that helical peptides could in principle also be used as starting point for the design of new therapeutic agents.…”

“…While these studies suggested that N‐locked agents could result in stable alpha‐helical binding agents, no binding studies on such constrained peptides have been reported thus far. Recently, we and others also proposed to introduce warheads into helical peptides to target Cys (Barile et al, ; Stebbins et al, ) or Lys residues (Baggio et al, ), resulting in very potent and selective agents. Hence, as an application, we derived N‐locked covalent BH3 peptides that can target the anti‐apoptotic protein Bfl‐1.…”

Covalent Small Molecules as Enabling Platforms for Drug Discovery

“…Some of these warheads can exhibit surprising aqueous stability, supporting their use in biological systems . Additionally, these warheads can result in improved selectivity relative to structurally related reversible inhibitors . Serine, and other alcoholic side chains, have proven targetable by numerous electrophiles such as fluorophosphonates, sulfur(VI) centres, activated ureas, and carbamates .…”