Crystal‐Structure‐Guided Design of Self‐Assembling RNA Nanotriangles

RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base‐pair interactions. Herein, we report the crystal‐structure‐guided design of highly stable RNA nanotriangles that self‐assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so‐far smallest circularly closed nanoobject made entirely of double‐stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand‐responsive RNA switches, which offer the opportunity to control self‐assembly and dissociation.     

Structure‐Based Design of a Macrocyclic PROTAC

Constraining a molecule in its bioactive conformation via macrocyclization represents an attractive strategy to rationally design functional chemical probes. While this approach has been applied to enzyme inhibitors or receptor antagonists, to date it remains unprecedented for bifunctional molecules that bring proteins together, such as PROTAC degraders. Herein, we report the design and synthesis of a macrocyclic PROTAC by adding a cyclizing linker to the BET degrader MZ1. A co‐crystal structure of macroPROTAC‐1 bound in a ternary complex with VHL and the second bromodomain of Brd4 validated the rational design. Biophysical studies revealed enhanced discrimination between the second and the first bromodomains of BET proteins. Despite a 12‐fold loss of binary binding affinity for Brd4, macroPROTAC‐1 exhibited cellular activity comparable to MZ1. Our findings support macrocyclization as an advantageous strategy to enhance PROTAC degradation potency and selectivity between homologous targets.     

Antivitamins B12—A Structure‐ and Reactivity‐Based Concept

B₁₂‐antimetabolites are compounds that counteract the physiological effects of vitamin B₁₂ and related natural cobalamins. Presented here is a structure‐ and reactivity‐based concept of the specific ′antivitamins B₁₂′: it refers to analogues of vitamin B₁₂ that display high structural similarity to the vitamin and are ′locked chemically′ to prevent their metabolic conversion into the crucial organometallic B₁₂‐cofactors. Application of antivitamins B₁₂ to healthy laboratory animals is, thus, expected to induce symptoms of B₁₂‐deficiency. Antivitamins B₁₂ may, hence, be helpful in elucidating still largely puzzling pathophysiological phenomena associated with B₁₂‐deficiency, and also in recognizing physiological roles of B₁₂ that probably still remain to be discovered.     

Electron Cryo‐microscopy as a Tool for Structure‐Based Drug Development

For decades, X‐ray crystallography and NMR have been the most important techniques for studying the atomic structure of macromolecules. However, as a result of size, instability, low yield, and other factors, many macromolecules are difficult to crystallize or unsuitable for NMR studies. Electron cryo‐microscopy (cryo‐EM) does not depend on crystals and has therefore been the method of choice for many macromolecular complexes that cannot be crystallized, but atomic resolution has mostly been beyond its reach. A new generation of detectors that are capable of sensing directly the incident electrons has recently revolutionized the field, with structures of macromolecules now routinely being solved to near‐atomic resolution. In this review, we summarize some of the most recent examples of high‐resolution cryo‐EM structures. We put particular emphasis on proteins with pharmacological relevance that have traditionally been inaccessible to crystallography. Furthermore, we discuss examples where interactions with small molecules have been fully characterized at atomic resolution. Finally, we stress the current limits of cryo‐EM, and methodological issues related to its usage as a tool for drug development.     

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to their substrate specificity. Swapping such active‐site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X‐ray structures and enzyme kinetics suggests a role of the active‐site residues in substrate recognition. Such a divergent active‐site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.     

Highly Efficient Synthesis of Multiantennary Bisected N‐glycans Based on Imidates

The occurrence of N‐glycans with a bisecting GlcNAc modification on glycoproteins has many implications in developmental and immune biology. However, these particular N‐glycans are difficult to obtain either from nature or through synthesis. We have developed a flexible and general method for synthesizing bisected N‐glycans of the complex type by employing modular TFAc‐protected donors for all antennae. The TFAc‐protected N‐glycans are suitable for the late introduction of a bisecting GlcNAc. This integrated strategy permits for the first time the use of a single approach for multiantennary N‐glycans as well as their bisected derivatives via imidates, with unprecedented yields even in a one‐pot double glycosylation. With this new method, rare N‐glycans of the bisected type can be obtained readily, thereby providing defined tools to decipher the biological roles of bisecting GlcNAc modifications.     

Rational Structure‐Based Design of Bright GFP‐Based Complexes with Tunable Dimerization

Fluorescent proteins are transformative tools; thus, any brightness increase is a welcome improvement. We invented the “vGFP strategy” based on structural analysis of GFP bound to a single‐domain antibody, predicting tunable dimerization, enhanced brightness (ca. 50 %), and improved pH resistance. We verified all of these predictions using biochemistry, crystallography, and single‐molecule studies. We applied the vsfGFP proteins in three diverse scenarios: single‐step immunofluorescence in vitro (3× brighter due to dimerization); expression in bacteria and human cells in vivo (1.5× brighter); and protein fusions showing better pH resistance in human cells in vivo. The vGFP strategy thus allows upgrading of existing applications, is applicable to other fluorescent proteins, and suggests a method for tuning dimerization of arbitrary proteins and optimizing protein properties in general.     

Protein‐Based Capacitive Biosensors: a New Tool for Structure‐Activity Relationship Studies

The present work reports a new application of a protein‐based capacitive biosensor as an in vitro assay for the selectivity study of the bacterial periplasmic protein MerP and four MerP variants. The modified MerP proteins were produced by site‐directed mutagenesis of the heavy metal associated motif (HMA). The MerP and modified MerPs selectivity for copper, zinc, cadmium and mercury bivalent ions were investigated and compared. The variations in the proteins affinity were related to the primary structure of the HMA motifs. Key amino acids for copper coordination of metalloproteins that contain the metal binding sequence Gly‐Met‐Thr‐Cys‐xxx‐xxx‐Cys were identified. The results brought insights valid for Menkes and Wilson ATPases. The protein‐based capacitive biosensors were a simple and useful tool for studying structure‐activity relationships of proteins.     

Multiple Keys for a Single Lock: The Unusual Structural Plasticity of the Nucleotidyltransferase (4′)/Kanamycin Complex

The most common mode of bacterial resistance to aminoglycoside antibiotics is the enzyme‐catalysed chemical modification of the drug. Over the last two decades, significant efforts in medicinal chemistry have been focused on the design of non‐ inactivable antibiotics. Unfortunately, this strategy has met with limited success on account of the remarkably wide substrate specificity of aminoglycoside‐modifying enzymes. To understand the mechanisms behind substrate promiscuity, we have performed a comprehensive experimental and theoretical analysis of the molecular‐recognition processes that lead to antibiotic inactivation by Staphylococcus aureus nucleotidyltransferase 4′(ANT(4′)), a clinically relevant protein. According to our results, the ability of this enzyme to inactivate structurally diverse polycationic molecules relies on three specific features of the catalytic region. First, the dominant role of electrostatics in aminoglycoside recognition, in combination with the significant extension of the enzyme anionic regions, confers to the protein/antibiotic complex a highly dynamic character. The motion deduced for the bound antibiotic seem to be essential for the enzyme action and probably provide a mechanism to explore alternative drug inactivation modes. Second, the nucleotide recognition is exclusively mediated by the inorganic fragment. In fact, even inorganic triphosphate can be employed as a substrate. Third, ANT(4′) seems to be equipped with a duplicated basic catalyst that is able to promote drug inactivation through different reactive geometries. This particular combination of features explains the enzyme versatility and renders the design of non‐inactivable derivatives a challenging task.     

Transition‐State Stabilization by a Secondary Substrate–Ligand Interaction: A New Design Principle for Highly Efficient Transition‐Metal Catalysis

A library of monodentate phosphane ligands, each bearing a guanidine receptor unit for carboxylates, was designed. Screening of the library gave some excellent catalysts for regioselective hydroformylation of β,γ‐unsaturated carboxylic acids. A terminal alkene, but‐3‐enoic acid, was hydroformylated with a linear/branched (l/b) regioselectivity up to 41. An internal alkene, pent‐3‐enoic acid was hydroformylated with regioselectivity up to 18:1. Further substrate selectivity (e.g., acid vs. methyl ester) and reaction site selectivity (monofunctionalization of 2‐vinylhept‐2‐enoic acid) were also achieved. Exploration of the structure–activity relationship and a practical and theoretical mechanistic study gave us an insight into the nature of the supramolecular guanidinium–carboxylate interaction within the catalytic system. This allowed us to identify a selective transition‐state stabilization by a secondary substrate–ligand interaction as the basis for catalyst activity and selectivity.