Stuart L. Warriner

Oligobenzamide proteomimetic inhibitors of the p53–hDM2 protein–protein interaction

Developing general strategies for inhibition of protein–protein interactions is a key challenge in chemical biology. Herein we describe oligobenzamide inhibitors of the p53–hDM2 protein–protein interaction.

Optimizing protein stability in vivo.

Identifying mutations that stabilize proteins is challenging because most substitutions are destabilizing. In addition to being of immense practical utility, the ability to evolve protein stability in vivo may indicate how evolution has formed todays protein sequences. Here we describe a genetic selection that directly links the in vivo stability of proteins to antibiotic resistance. It allows the identification of stabilizing mutations within proteins. The large majority of mutants selected for improved antibiotic resistance are stabilized both thermodynamically and kinetically, indicating that similar principles govern stability in vivo and in vitro. The approach requires no prior structural or functional knowledge and allows selection for stability without a need to maintain function. Mutations that enhance thermodynamic stability of the protein Im7 map overwhelmingly to surface residues involved in binding to colicin E7, showing how the evolutionary pressures that drive Im7-E7 complex formation have compromised the stability of the isolated Im7 protein.

Getting a camel through the eye of a needle: the import of folded proteins by peroxisomes.

Peroxisomes are a family of organelles which have many unusual features. They can arise de novo from the endoplasmic reticulum by a still poorly characterized process, yet possess a unique machinery for the import of their matrix proteins. As peroxisomes lack DNA, their function, which is highly variable and dependent on developmental and/or environmental conditions, is determined by the post‐translational import of specific metabolic enzymes in folded or oligomeric states. The two classes of matrix targeting signals for peroxisomal proteins [PTS1 (peroxisomal targeting signal 1) and PTS2] are recognized by cytosolic receptors [PEX5 (peroxin 5) and PEX7 respectively] which escort their cargo proteins to, or possibly across, the peroxisome membrane. Although the membrane translocation mechanism remains unclear, it appears to be driven by thermodynamically favourable binding interactions. Recycling of the receptors from the peroxisome membrane requires ATP hydrolysis for two linked processes: ubiquitination of PEX5 (and the PEX7 co‐receptors in yeast) and the function of two peroxisome‐associated AAA (ATPase associated with various cellular activities) ATPases, which play a role in recycling or turnover of the ubiquitinated receptors. This review summarizes and integrates recent findings on peroxisome matrix protein import from yeast, plant and mammalian model systems, and discusses some of the gaps in our understanding of this remarkable protein transport system.

Synthesis of functionalised aromatic oligamide rods

A current goal in synthetic chemistry is the design and synthesis of molecules that adopt well defined conformations-so called foldamers. In this manuscript we describe a modular approach for construction of rod shaped para-oligobenzamide molecules. Our approach permits regiospecific incorporation of side chains through a phenolic ether linkage on the scaffold; a feature that partly restricts the conformation of the rod through intramolecular hydrogen-bonding.

Tuning glycoside reactivity: New tool for efficient oligosaccharide synthesis

The concise preparation of complex oligosaccharides remains a significant challenge for synthetic organic chemistry. The tuning of donor reactivity during coupling reactions, such that we may avoid the lengthy protecting-group manipulations of classical carbohydrate synthesis, affords a strategy for the rapid assembly of large sugar systems. Competition reactions have been used to quantify the influence of protecting groups, monosaccharide type, and anomeric leaving groups on the reactivity of various glycosyl donors.

Solvent-Dependent Self-Assembly Behaviour and Speciation Control of Pd6L8 Metallo-supramolecular Cages

The C3-symmetric chiral propylated host-type ligands (±)-tris(isonicotinoyl)-tris(propyl)-cyclotricatechylene (L1) and (±)-tris(4-pyridyl-4-benzoxy)-tris(propyl)-cyclotricatechylene (L2) self-assemble with Pd(II) into [Pd6L8](12+) metallo-cages that resemble a stella octangula. The self-assembly of the [Pd6(L1)8](12+) cage is solvent-dependent; broad NMR resonances and a disordered crystal structure indicate no chiral self-sorting of the ligand enantiomers in DMSO solution, but sharp NMR resonances occur in MeCN or MeNO2. The [Pd6(L1)8](12+) cage is observed to be less favourable in the presence of additional ligand, than is its counterpart, where L=(±)-tris(isonicotinoyl)cyclotriguaiacylene (L1 a). The stoichiometry of reactant mixtures and chemical triggers can be used to control formation of mixtures of homoleptic or heteroleptic [Pd6L8](12+) metallo-cages where L=L1 and L1 a.

Small-molecule proteomimetic inhibitors of the HIF-1α-p300 protein-protein interaction.

The therapeutically relevant hypoxia inducible factor HIF‐1α–p300 protein–protein interaction can be orthosterically inhibited with α‐helix mimetics based on an oligoamide scaffold that recapitulates essential features of the C‐terminal helix of the HIF‐1α C‐TAD (C‐terminal transactivation domain). Preliminary SAR studies demonstrated the important role of side‐chain size and hydrophobicity/hydrophilicity in determining potency. These small molecules represent the first biophysically characterised HIF‐1α–p300 PPI inhibitors and the first examples of small‐molecule aromatic oligoamide helix mimetics to be shown to have a selective binding profile. Although the compounds were less potent than HIF‐1α, the result is still remarkable in that the mimetic reproduces only three residues from the 42‐residue HIF‐1α C‐TAD from which it is derived.

Solid‐Phase Methodology for Synthesis of O‐Alkylated Aromatic Oligoamide Inhibitors of α‐Helix‐Mediated Protein–Protein Interactions

Rapid access to rigid rods: A method is described for the synthesis of 3-O-alkylated aromatic oligobenzamide foldamers that could be used for assembly of libraries of α-helix mimetic inhibitors of protein-protein interactions (see scheme; Fmoc=9-fluorenylmethoxycarbonyl).

A Protein-Based Pentavalent Inhibitor of the Cholera Toxin B-Subunit

Protein toxins produced by bacteria are the cause of many life-threatening diarrheal diseases. Many of these toxins, including cholera toxin (CT), enter the cell by first binding to glycolipids in the cell membrane. Inhibiting these multivalent protein/carbohydrate interactions would prevent the toxin from entering cells and causing diarrhea. Here we demonstrate that the site-specific modification of a protein scaffold, which is perfectly matched in both size and valency to the target toxin, provides a convenient route to an effective multivalent inhibitor. The resulting pentavalent neoglycoprotein displays an inhibition potency (IC50) of 104 pm for the CT B-subunit (CTB), which is the most potent pentavalent inhibitor for this target reported thus far. Complexation of the inhibitor and CTB resulted in a protein heterodimer. This inhibition strategy can potentially be applied to many multivalent receptors and also opens up new possibilities for protein assembly strategies.

Residual ligand entropy in the binding of p-substituted benzenesulfonamide ligands to bovine carbonic anhydrase II.

In studies on the thermodynamics of ligand-protein interactions, it is often assumed that the configurational and conformational entropy of the ligand is zero in the bound state (i.e., the ligand is rigidly fixed in the binding pocket). However, there is little direct experimental evidence for this assumption, and in the case of binding of p-substituted benzenesulfonamide inhibitors to bovine carbonic anhydrase II (BCA II), the observed thermodynamic binding signature derived from isothermal titration calorimetry experiments leads indirectly to the conclusion that a considerable degree of residual entropy remains in the bound ligand. Specifically, the entropy of binding increases with glycine chain length n, and strong evidence exists that this thermodynamic signature is not driven by solvent reorganization. By use of heteronuclear (15)N NMR relaxation measurements in a series (n = 1-6) of (15)N-glycine-enriched ligands, we find that the observed thermodynamic binding signature cannot be explained by residual ligand dynamics in the bound state, but rather results from the indirect influence of ligand chain length on protein dynamics.