Sébastien Ulrich

Oxime ligation: a chemoselective click-type reaction for accessing multifunctional biomolecular constructs.

There is a growing need for biocompatible click reactions in order to prepare multifunctional conjugates, which are valuable molecules for innovative biomedical applications. In this context, we review the recent advances in the implementation of oxime ligation for the synthesis of multivalent or multicomponent systems. The value of these products is emphasized by their use in cell targeting, imaging, synthetic vaccines, and surface modifications.

Adaptation to Shape Switching by Component Selection in a Constitutional Dynamic System

Molecules having different accessible shape states, which can be addressed in an effector-controlled manner, may be termed morphological switches. A dynamic covalent system can undergo adaptation to each state of a two-state morphological switch by generation of an optimal constitution through component selection. We have studied such a component selection in the dynamic covalent constituents generated by metal cation-induced shape switching of a core component between two states of W and U shape, characterized by both different geometries and different coordination features. The system performs shape-dependent self-sorting of metal ions and components. The origin of the selectivity was investigated through competition experiments, in solution and by analysis of solid state structures, which reveal the role of the molecular shape in the formation of a particular self-assembled architecture. The coordination features of each state as well as phase change also play an important role, in addition to the shape plasticity, in steering the covalent dynamic system toward the formation of a given entity by the selection of the most appropriate components. Different examples are described which show that the morphological switching of one component of a given self-assembled entity can lead to the exchange of the complementary one, which is no longer the best partner, for a new partner, able to form a more stable new assembly. Thus, the constitutional evolution of these dynamic systems is steered by the shape of a given state via both its geometry and its coordination features toward metal ions, leading to incorporation/decorporation of the most appropriate components. The controlled interconversion of the shape states of the morphological switches, induced by addition/removal of metal ions, results in a constitutional adaptation behavior through inversion of the selection preferences.

Adaptation and Optical Signal Generation in a Constitutional Dynamic Network

Self-sorting dynamic library: The effector-induced modulation of the shape and constitution of the members of a constitutional dynamic network (see scheme) allows for the regulation of the interconnected constituents and for the control of an emergent function, here the generation of an optical output which originates from a charge-transfer interaction.

Reversible constitutional switching between macrocycles and polymers induced by shape change in a dynamic covalent system

We report here the development of morphological switches as a new tool that can be used in constitutional dynamic chemistry (CDC) to control the constitution of the whole dynamic system. Molecules that have well-defined but switchable shapes were designed and synthesized. Their restrained conformational states were characterized both in the solid and in solution. The addition of metal ions induces a shape change through coordination; the shape generated was also fully investigated both in the solid and in solution. Such molecules constitute morphological switches, meaning that they can explore various shape states as a result of controlled well-defined shape changes triggered by an effector. These morphological switches were then integrated into covalent dynamic systems through formation of reversible imine bonds. Thermodynamic and kinetic analyses were performed in order to quantify the covalent equilibrium and to investigate the labile character of the covalent reversible link. It was then demonstrated that the molecular shape state of the morphological switches induces a well-defined constitution through covalent self-assembly, and that the system can be steered, quantitatively and reversibly without significant fatigue, between two different constitutional states, respectively, polymeric and macrocyclic assemblies. The dynamic covalent polymeric assemblies were analysed by DOSY NMR and small angle neutrons scattering (SANS). Their dynamic behaviour as a function of the concentration and the temperature was demonstrated and characterized.

Probing secondary interactions in biomolecular recognition by dynamic combinatorial chemistry

Artificial multivalent recognition systems offer promising perspectives for developing synthetic compounds capable of interacting effectively and selectively with biomolecules in aqueous medium. The identification of multi-point binding ligands requires screening of a large number of complex structures, with different spacers, different ligands, and varying valency. This represents a challenge for rational design approaches. On the other hand, the use of dynamic covalent chemistry enables a target-driven one-pot screening approach for probing secondary interactions, thereby facilitating the identification of multivalent recognition systems that optimally combine multiple fragments. Herein we review the recent developments in the implementation of dynamic combinatorial chemistry for probing secondary interactions and thereby identify multi-point binding ligands of biomolecules.

Degradable Hybrid Materials Based on Cationic Acylhydrazone Dynamic Covalent Polymers Promote DNA Complexation through Multivalent Interactions

The design of smart nonviral vectors for gene delivery is of prime importance for the successful implementation of gene therapies. In particular, degradable analogues of macromolecules represent promising targets as they would combine the multivalent presentation of multiple binding units that is necessary for achieving effective complexation of therapeutic oligonucleotides with the controlled degradation of the vector that would in turn trigger drug release. Toward this end, we have designed and synthesized hybrid polyacylhydrazone-based dynamic materials that combine bis-functionalized cationic monomers with ethylene oxide containing monomers. Polymer formation was characterized by (1) H and DOSY NMR spectroscopy and was found to take place at high concentration, whereas macrocycles were predominantly formed at low concentration. HPLC monitoring of solutions of these materials in aqueous buffers at pH values ranging from 5.0 to 7.0 revealed their acid-catalyzed degradation. An ethidium bromide displacement assay and gel electrophoresis clearly demonstrated that, despite being dynamic, these materials are capable of effectively complexing dsDNA in aqueous buffer and biological serum at N/P ratios comparable to polyethyleneimine polymers. The self-assembly of dynamic covalent polymers through the incorporation of a reversible covalent bond within their main chain is therefore a promising strategy for generating degradable materials that are capable of establishing multivalent interactions and effectively complexing dsDNA in biological media.

Dynamic Expression of DNA Complexation with Self-assembled Biomolecular Clusters†

We report herein the implementation of a dynamic covalent chemistry approach to the generation of multivalent clusters for DNA recognition. We show that biomolecular clusters can be expressed in situ by a programmed self-assembly process using chemoselective ligations. The cationic clusters are shown, by fluorescence displacement assay, gel electrophoresis and isothermal titration calorimetry, to effectively complex DNA through multivalent interactions. The reversibility of the ligation was exploited to demonstrate that template effects occur, whereby DNA imposes component selection in order to favor the most active DNA-binding clusters. Furthermore, we show that a chemical effector can be used to trigger DNA release through component exchange reactions.

Fluorescent Silica Nanoparticles with Multivalent Inhibitory Effects towards Carbonic Anhydrases

Multifunctional silica nanoparticles decorated with fluorescent and sulfonamide carbonic anhydrase (CA) inhibitors were prepared and investigated as multivalent enzyme inhibitors against the cytosolic isoforms hCA I and II and the transmembrane tumor-associated ones hCA IX and XII. Excellent inhibitory effects were observed with these nanoparticles, with KI values in the low nanomolar range (6.2-0.67 nM) against all tested isozymes. A significant multivalency effect was seen for the inhibition of the monomeric enzymes hCA I and II compared to the dimeric hCA IX and hCA XII isoforms, where no multivalent effect was observed, suggesting that the multivalent binding is occurring through enzyme clustering.

Importance of Steric Effects on the Efficiency and Fidelity of Transcription by T7 RNA Polymerase

DNA-dependent RNA polymerases such as T7 RNA polymerase (T7 RNAP) perform the transcription of DNA into mRNA with high efficiency and high fidelity. Although structural studies have provided a detailed account of the molecular basis of transcription, the relative importance of factors like hydrogen bonds and steric effects remains poorly understood. We report herein the first study aimed at systematically probing the importance of steric and electrostatic effects on the efficiency and fidelity of DNA transcription by T7 RNAP. We used synthetic nonpolar analogues of thymine with sizes varying in subangstrom increments to probe the steric requirements of T7 RNAP during the elongation mode of transcription. Enzymatic assays with internal radiolabeling were performed to compare the efficiency of transcription of modified DNA templates with a natural template containing thymine as a reference. Furthermore, we analyzed effects on the fidelity by measuring the composition of RNA transcripts by enzymatic digestion followed by two-dimensional thin layer chromatography separation. Our results demonstrate that hydrogen bonds play an important role in the efficiency of transcription but, interestingly, do not appear to be required for faithful transcription. Steric effects (size and shape variations) are found to be significant both in insertion of a new RNA base and in extension beyond it.

Biodistribution and Pharmacokinetic Studies of a Porphyrin Dimer Photosensitizer (Oxdime) by Fluorescence Imaging and Spectroscopy in Mice Bearing Xenograft Tumors

Herein, we present a study of the pharmacokinetics and biodistribution of a butadiyne‐linked conjugated porphyrin dimer (Oxdime) designed to have high near‐infrared (NIR) 2‐photon absorption cross‐section for photodynamic therapy (PDT). Changes in biodistribution over time were monitored in mice carrying B16‐F10 melanoma xenografts, following intravenous injection. Using fluorescence imaging of live animals and analyzing isolated organs ex vivo at different time points between 30 min and 24 h after injection, accumulation of Oxdime was measured in several organs (heart, kidney and liver) and in tumor. The concentration in the plasma was about 5–10 times higher than in other tissues. The fluorescence signal peaked at 3–12 h after injection in most tissues, including the tumor and the plasma. The change in the fluorescence emission spectrum of the sensitizer over time was also monitored and a shift in the maximum from 800 to 740 nm was observed over 24 h, showing that the Oxdime is metabolized. Significant quantities accumulated in the tumor, indicating that this PDT sensitizer may be promising for cancer treatment.