One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

The increasing availability of experimental and computational protein structures entices their use for function prediction. Here we develop an automated procedure to identify enzymes involved in metabolic reactions by assessing substrate conformations docked to a library of protein structures. By screening AlphaFold-modeled vitamin B6-dependent enzymes, we find that a metric based on catalytically favorable conformations at the enzyme active site performs best (AUROC Score=0.84) in identifying genes associated with known reactions. Applying this procedure, we identify the mammalian gene encoding hydroxytrimethyllysine aldolase (HTMLA), the second enzyme of carnitine biosynthesis. Upon experimental validation, we find that the top-ranked candidates, serine hydroxymethyl transferase (SHMT) 1 and 2, catalyze the HTMLA reaction. However, a mouse protein absent in humans (threonine aldolase; Tha1) catalyzes the reaction more efficiently. Tha1 did not rank highest based on the AlphaFold model, but its rank improved to second place using the experimental crystal structure we determined at 2.26 Å resolution. Our findings suggest that humans have lost a gene involved in carnitine biosynthesis, with HTMLA activity of SHMT partially compensating for its function.

Deciphering the role of recurrent FAD-dependent enzymes in bacterial phosphonate catabolism.

Phosphonates-compounds containing a direct C-P bond-represent an important source of phosphorus in some environments. The most common natural phosphonate is 2-aminoethylphosphonate (AEP). Many bacteria can break AEP down through specialized "hydrolytic" pathways, which start with the conversion of AEP into phosphonoacetaldehyde (PAA), catalyzed by the transaminase PhnW. However, the substrate scope of these pathways is very narrow, as PhnW cannot process other common AEP-related phosphonates, notably N-methyl AEP (M1AEP). Here, we describe a heterogeneous group of FAD-dependent oxidoreductases that efficiently oxidize M1AEP to directly generate PAA, thus expanding the versatility and usefulness of the hydrolytic AEP degradation pathways. Furthermore, some of these enzymes can also efficiently oxidize plain AEP. By doing so, they surrogate the role of PhnW in organisms that do not possess the transaminase and create novel versions of the AEP degradation pathways in which PAA is generated solely by oxidative deamination.

Gold(I)-catalysed hydroarylations of alkynes for the synthesis of inherently chiral calix[4]arenes.

We describe the first gold(I)-catalysed intramolecular hydroarylation of alkynes for the straightforward synthesis of inherently chiral calix[4]arenes. This step- and atom-economical approach, which exploits a formal meta-functionalisation of the calix[4]arene macrocycle, is able to deliver an ample family of N-heterocyclic, chiral compounds in high yields and functional group tolerance.

Selective enhancement of organic dye properties through encapsulation in rotaxane orientational isomers.

We report the synthesis and characterisation of [2]rotaxanes based on a stilbazolium dye and a calix[6]arene macrocycle. Since both components are non-symmetric, two orientational isomers are obtained. The two isomers display distinct photophysical and photochemical properties in solution and solid state, superior to the unencapsulated dye.

Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions.

Coevolution at the gene level, as reflected by correlated events of gene loss or gain, can be revealed by phylogenetic profile analysis. The optimal method and metric for comparing phylogenetic profiles, especially in eukaryotic genomes, are not yet established. Here, we describe a procedure suitable for large-scale analysis, which can reveal coevolution based on the assessment of the statistical significance of correlated presence/absence transitions between gene pairs. This metric can identify coevolution in profiles with low overall similarities and is not affected by similarities lacking coevolutionary information. We applied the procedure to a large collection of 60,912 orthologous gene groups (orthogroups) in 1,264 eukaryotic genomes extracted from OrthoDB. We found significant cotransition scores for 7,825 orthogroups associated in 2,401 coevolving modules linking known and unknown genes in protein complexes and biological pathways. To demonstrate the ability of the method to predict hidden gene associations, we validated through experiments the involvement of vertebrate malate synthase-like genes in the conversion of (S)-ureidoglycolate into glyoxylate and urea, the last step of purine catabolism. This identification explains the presence of glyoxylate cycle genes in metazoa and suggests an anaplerotic role of purine degradation in early eukaryotes.

A Multiresponsive Calix[6]arene Pseudorotaxane Empowered by Fluorophoric Dansyl Groups.

We report the synthesis and characterization, by means of NMR and UV-visible spectroscopy and electrochemical techniques, of a dansyl calix[6]arene derivative and of its pseudorotaxane complex with a bipyridinium-based axle. This novel macrocycle shows remarkable complexation ability, in analogy with parent compounds, while the dansyl moieties impart valuable features to the system. Indeed, these units: i) signal the state of the system by fluorescence; ii) can be reversibly protonated, enabling the modulation of the complexation abilities of the macrocycle; iii) participate in photoinduced electron transfer processes, which may be exploited to tune the stability of the supramolecular complex. Therefore, in this multiresponsive pseudorotaxane, the threading and de-threading motions of the molecular components can be modulated either by protonation of the calixarene host or by reduction of the bipyridinium guest, which can be accomplished both by electrochemical reduction and via photoinduced electron transfer. Overall, three orthogonal and reversible stimuli can be used to induce molecular movements of the pseudorotaxane components.

Calix[6]arene-Based [3]Rotaxanes as Prototypes for the Template Synthesis of Molecular Capsules.

In this work, the ability of several bis-viologen axles to thread a series of heteroditopic tris(N-phenylureido)calix[6]arene wheels to give interwoven supramolecular complexes to the [3]pseudorotaxane type was studied. The unidirectionality of the threading process inside these nonsymmetric wheels allows the formation of highly preorganised [3]pseudorotaxane and [3]rotaxane species in which the macrocycles phenylureido moieties, functionalised with either ester, carboxylic, or hydroxymethyl groups, are facing each other. As verified by NMR and semiempirical computational studies, these latter compounds possess the correct spatial arrangement of their subcomponents, which could lead, in principle, upon proper bridging reaction, to the realisation of upper-to-upper molecular capsules that are based on calix[6]arene derivatives.

Triazole-enabled, iron-catalysed linear/branched selective C-H alkylations with alkenes.

Iron-catalysed C-H alkylations with alkenes were achieved on benzamides by N-triazole assistance. A notable switch of the regioselectivity from linear to branched was observed depending on the nature of the olefin employed. The approach allowed for the synthesis of a family of decorated benzamides with ample scope and high levels of chemo-, regio- and site-selectivity.

Autonomous Non-Equilibrium Self-Assembly and Molecular Movements Powered by Electrical Energy.

The ability to exploit energy autonomously is one of the hallmarks of life. Mastering such processes in artificial nanosystems can open technological opportunities. In the last decades, light- and chemically driven autonomous systems have been developed in relation to conformational motion and self-assembly, mostly in relation to molecular motors. In contrast, despite electrical energy being an attractive energy source to power nanosystems, its autonomous harnessing has received little attention. Herein we consider an operation mode that allows the autonomous exploitation of electrical energy by a self-assembling system. Threading and dethreading motions of a pseudorotaxane take place autonomously in solution, powered by the current flowing between the electrodes of a scanning electrochemical microscope. The underlying autonomous energy ratchet mechanism drives the self-assembly steps away from equilibrium with a higher energy efficiency compared to other autonomous systems. The strategy is general and might be extended to other redox-driven systems.

Diametric calix[6]arene gold(I) catalysts for intramolecular cyclopropanations of 1,6-dienynes.

We report a solid-state structural investigation of diametric calix[6]arene-based phosphine gold(I) cavitands which are characterised by two specific, different 1,2,3-alternate conformations in solution and in the solid state. The effect of the specific orientation of phosphines, with respect to macrocycles, was studied in intramolecular cyclopropanation of 1,6-dienynes. The general applicability of these catalysts was disclosed, delivering a family of polycycles with high yields and functional group tolerance.

Diametric calix[6]arene-based phosphine gold(I) cavitands.

We report the synthesis and characterization, in low polarity solvents, of a novel class of diametric phosphine gold(I) cavitands characterized by a 1,2,3-alternate geometry. Preliminary catalytic studies were performed on a model cycloisomerization of 1,6-enynes as a function of the relative orientation of the bonded gold(I) nuclei with respect to the macrocyclic cavity.

Multi-Dimensional Quantum Capacitance of the Two-Site Hubbard Model: The Role of Tunable Interdot Tunneling.

Few-electron states confined in quantum-dot arrays are key objects in quantum computing. The discrimination between these states is essential for the readout of a (multi-)qubit state, and can be achieved through a measurement of the quantum capacitance within the gate-reflectometry approach. For a system controlled by several gates, the dependence of the measured capacitance on the direction of the oscillations in the voltage space is captured by the quantum capacitance matrix. Herein, we apply this tool to study a double quantum dot coupled to three gates, which enable the tuning of both the bias and the tunneling between the two dots. Analytical solutions for the two-electron case are derived within a Hubbard model, showing the overall dependence of the quantum capacitance matrix on the applied gate voltages. In particular, we investigate the role of the tunneling gate and reveal the possibility of exploiting interdot coherences in addition to charge displacements between the dots. Our results can be directly applied to double-dot experimental setups, and pave the way for further applications to larger arrays of quantum dots.

Selective access to constitutionally identical, orientationally isomeric calix[6]arene-based [3]rotaxanes by an active template approach.

Tris(phenylureido)calix[6]arene is endowed with unique properties that make it a valuable macrocyclic component for the synthesis of mechanically interlocked molecules. Its three-dimensional and intrinsically nonsymmetric structure is kinetically selective toward two processes: (i) in apolar media, the threading of bipyridinium based axle-like components takes place exclusively from the upper rim; (ii) SN2 alkylation reactions of a pyridylpyridinium precursor engulfed in the cavity occur selectively at pyridylpyridinium nitrogen atom located at the macrocycle upper rim (active template synthesis). Here we exploit such properties to prepare two series of [3]rotaxanes, each consisting of three sequence isomers that arise from the threading of two identical but nonsymmetric wheels on a symmetric thread differing only for the reciprocal orientation of the macrocycles. The features of the calix[6]arene and the active template synthetic approach, together with a careful selection of the precursors, enabled us to selectively synthesise the [3]rotaxane sequence isomers of each series with fast kinetics and high yields.

Calixarene-based artificial ionophores for chloride transport across natural liposomal bilayer: Synthesis, structure-function relationships, and computational study.

An amphiphilic calix[6]arene, alone or complexed with an axle to form a pseudo-rotaxane, has been embedded into liposomes prepared from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and the permeability of the membrane-doped liposomes towards Cl- ions has been evaluated by using lucigenin as the fluorescent probe. The pseudo-rotaxane promotes transmembrane transport of Cl- ions more than calix[6]arene does. Surprisingly, the quenching of lucigenin was very fast for liposomes doped with the positively charged axle alone. Molecular dynamics (MD) simulations and quantum-chemical calculations were also carried out for providing a semi-quantitative support to the experimental results.

Merging Molecular Recognition and Gold(I) Catalysis with Triphoscalix[6]arene Ligands.

We report the synthesis and characterization of novel triphosphine calix[6]arene ligands. These supramolecular wheels, with recognition features governed by the hydrogen-bonding domain, were employed to synthesize multitasking trinuclear gold(I) complexes as a new platform for the synthesis of interwoven (pseudo)rotaxane species. In parallel, the multivalent, metal-bonded upper rim displayed catalytic features promoting highly selective gold-catalyzed cycloisomerization reactions of 1,6-enynes.

Heteroditopic Calix[6]arene Based Intervowen and Interlocked Molecular Devices.

Since the dawn of supramolecular chemistry, calixarenes have been employed as platforms onto which functional groups and binding sites can be loaded in a regio- and stereocontrolled manner for the recognition of charged and neutral species. Despite their wider annulus, potentially suitable to bind larger guests, the larger members of the calixarene series have been relatively less employed, mainly because of the synthetic difficulties to control their conformational flexibility and their regioselective functionalization. In this account, we will present the achievements gained during the last two decades on the use of the calix[6]arene as a platform to build-up structures in which the macrocycle acts as a wheel for the synthesis of oriented (pseudo)rotaxanes. We also account on how these calix[6]arene hosts affect the reactivity or spectroscopic properties of their bound guests.

Calix[6]arene-based Brønsted acids for molecular recognition and catalysis.

We report the synthesis of a versatile trifluoromethylsulfonamide calix[6]arene derivative with Brønsted acid features which can influence both molecular recognition and catalytic application. Indeed, in low polarity media, the trifluoromethyl-containing supramolecular wheel is able to respond to the complexation with charged species as a function of its selective ion-pair recognition. In parallel, the enhanced acidity is the key to promote Michael additions of indoles to nitroalkenes under pseudo-physiological reaction conditions (H2O, 37 °C).

Trisulfonamide calix[6]arene-catalysed Michael addition to nitroalkenes.

We describe the application of a novel family of trisulfonamide (TSA) calix[6]arenes in general acid catalysis. Hydrogen-bonding interactions between acidic TSA and methanol boosted the reactivity of the Michael addition of indoles to nitroalkene derivatives. The transformation occurs at a low catalyst loading of 5 mol%, allowing for the synthesis of nitroalkanes with good yields and functional group tolerance.

Ion-Pair Selective Conformational Rearrangement of Sulfonamide Calix[6]arene-Based Pseudorotaxanes.

We describe the synthesis of a new class of trisulfonamide calix[6]arene-based wheels that can bind dialkylviologen salts, in apolar media. The threading process occurs through a selective ion-pair recognition, established by the sulfonamide groups with the counterions of the bipyridinium salts, that dictates a conformational rearrangement of the corresponding pseudorotaxanes.

Tuning the Fluorescence Through Reorientation of the Axle in Calix[6]arene-Based Pseudorotaxanes.

This work describes a calix[6]arene-based wheel that binds, in non-polar media, a stilbazolium salt to yield a mixture of pseudorotaxane orientational isomers. The isomer's abundance ratio evolves with time and can be reversibly tuned by adjusting the temperature. The spectroscopic properties, and notably the emission spectrum, of the bound guest depend on its orientation inside the non-palindromic wheel, suggesting such a system as a switch with spectroscopic readout.