Volume 10 Issue 9, September 2014

The application of macrocycles to previously undruggable targets has aroused a great deal of interest in this structural class. Recent studies advance our understanding of the way macrocycles bind protein targets and provide new strategies and tools to generate peptide-based macrocycles.

Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory neurotransmission, which is crucial for memory and learning. New cryo-electron microscopy structures of these receptors trapped in distinct functional states provide remarkable insight into conformational changes triggered by agonist binding.

Besides signaling from the plasma membrane, evidence for noncanonical signaling by GPCRs from internal compartments has recently emerged and is highlighted in this Perspective. For the well-studied PTHR, agonists stabilize a distinct receptor conformation within endosomes, leading to sustained signaling.

A GPCR, the parathyroid hormone receptor, can elicit a sustained signal from internal membranes after internalization. The signal was found to be terminated by a feedback mechanism where PKA activates the proton pump v-ATPase, which acidifies endosomes.

Finding evolutionary links between protein superfamilies has proven challenging. Advanced bioinformatics tools now identify relationships across two superfolds as well as a hybrid family whose structure displays characteristics of both.

Protein-protein interfaces are stabilized by ‘hot spots’ of interactions; helices that drive some of these interactions have been used as inspiration for peptide inhibitors. A computational program called ‘LoopFinder’ now identifies protein loops that perform equivalent roles, revealing new opportunities to explore biology.

Macrocycles have the potential to act on currently undruggable targets, but their discovery thus far has been unsystematic. A physicochemical analysis of all nonredundant co-crystal structures now sets out guidelines for macrocycle development.

Peptide macrocycles are attracting increasing attention as tools for research and as potential therapeutics. The highly efficient butelase 1—homologous to proteases but specific for ligations—offers a new method for peptide cyclization.

The twister ribozyme is a recently discovered self-cleaving RNA that has wide distribution in bacteria and eukaryotes. A crystal structure of a twister ribozyme reveals a double-pseudoknot core that positions a conserved guanine near the scissile phosphate where it participates in general acid-base catalysis.

A compound previously identified as a dopamine D2 receptor allosteric modulator was found to be a bitopic ligand that binds the orthosteric and allosteric sites to allow binding to one D2 protomer and allosteric modulation of the associated protomer.

SK potassium channels are activated by Ca²⁺-bound calmodulin (CaM) and regulated by phosphorylation. Electrophysiology and MD simulations show that a PIP₂-binding site formed at the interface of CaM and SK2, conferring PIP₂ sensitivity on the channels.

ABPP combined with quantitative MS enabled identification of specific on- and off-targets of covalent kinase inhibitors. Modifications to inhibitors that alter specificity beyond a defined window can promote kinase-independent toxicity.

A haploid screen in human cells identified the solute carrier protein family member, SLC35F2, as a determinant of the sensitivity of cells to the DNA damaging agent, YM155, by promoting YM155 import into cells.

A small-molecule compound, GSK2194069, specifically inhibits the β-ketoacyl reductase (KR) activity of the human fatty acid synthase. A co-crystal structure of the KR domain with the inhibitor confirms this interaction.

The bacterial ydaO riboswitch senses the second messenger c-di-AMP. Crystallographic and isothermal titration calorimetry analysis reveals that ydaO binds two molecules of c-di-AMP in binding pockets related by pseudo-two-fold symmetry.

Crystal structures of the ydaO riboswitch from two thermophilic bacteria reveal a square-shaped RNA architecture that is locked together by two c-di-AMP ligands that bind in pseudosymmetric binding pockets.