Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease.

Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.

Platinum(0)-η2-1,2-(E)ditosylethene Complexes Bearing Phosphine, Isocyanide and N-Heterocyclic Carbene Ligands: Synthesis and Cytotoxicity towards Ovarian and Breast Cancer Cells.

A wide range of platinum(0)-η2-(E)-1,2-ditosylethene complexes bearing isocyanide, phosphine and N-heterocyclic carbene ancillary ligands have been prepared with high yields and selectivity. All the novel products underwent thorough characterization using spectroscopic techniques, including NMR and FT-IR analyses. Additionally, for some compounds, the solid-state structures were elucidated through X-ray diffractometry. The synthesized complexes were successively evaluated for their potential as anticancer agents against two ovarian cancer cell lines (A2780 and A2780cis) and one breast cancer cell line (MDA-MB-231). The majority of the compounds displayed promising cytotoxicity within the micromolar range against A2780 and MDA-MB-231 cells, with IC50 values comparable to or even surpassing those of cisplatin. However, only a subset of compounds was cytotoxic against cisplatin-resistant cancer cells (A2780cis). Furthermore, the assessment of antiproliferative activity on MRC-5 normal cells revealed certain compounds to exhibit in vitro selectivity. Notably, complexes 3d, 6a and 6b showed low cytotoxicity towards normal cells (IC50 > 100 µM) while concurrently displaying potent cytotoxicity against cancer cells.

Rational Design of Palladium(II) Indenyl and Allyl Complexes Bearing Phosphine and Isocyanide Ancillary Ligands with Promising Antitumor Activity.

A new class of palladium-indenyl complexes characterized by the presence of one bulky alkyl isocyanide and one aryl phosphine serving as ancillary ligands has been prepared, presenting high yields and selectivity. All the new products were completely characterized using spectroscopic and spectrometric techniques (NMR, FT-IR, and HRMS), and, for most of them, it was also possible to define their solid-state structures via X-ray diffractometry, revealing that the indenyl fragment always binds to the metal centre with a hapticity intermediate between ƞ3 and ƞ5. A reactivity study carried out using piperidine as a nucleophilic agent proved that the indenyl moiety is the eligible site of attack rather than the isocyanide ligand or the metal centre. All complexes were tested as potential anticancer agents against three ovarian cancer cell lines (A2780, A2780cis, and OVCAR-5) and one breast cancer cell line (MDA-MB-231), displaying comparable activity with respect to cisplatin, which was used as a positive control. Moreover, the similar cytotoxicity observed towards A2780 and A2780cis cells (cisplatin-sensitive and cisplatin-resistant, respectively) suggests that our palladium derivatives presumably act with a mechanism of action different than that of the clinically approved platinum drugs. For comparison, we also synthesized Pd-ƞ3-allyl derivatives, which generally showed a slightly higher activity towards ovarian cancer cells and lower activity towards breast cancer cells with respect to their Pd-indenyl congeners.

Highly Efficient Electrochemiluminescence from Imidazole-Based Thermally Activated Delayed Fluorescence Emitters.

A family of novel thermally activated delayed fluorescence (TADF) emitters has been synthesized by a straightforward and metal-free synthesis, and structurally characterized. In this work we kept the acceptor moiety, 4-(1H-imidazol-1-yl)benzonitrile, fixed and systemically tested different donors to correlate their photophysical and electrochemical properties with their performance in electrochemiluminescence using both benzoyl peroxide as co-reactant and co-reactant free (annihilation) conditions. Some compounds exceeded the efficiency of the standard [Ru(bpy)3 ]Cl2 by up to 28 times with benzoyl peroxide and 38 times in annihilation. Interestingly, we found that the efficiency is mainly dictated by the electrochemical reversibility of the redox processes rather than by the photophysical properties in terms of photoluminescence quantum yields or excited-state lifetime. In addition, the annihilation electrochemiluminescence efficiency strongly depends on the pulse sequence. The imidazole moiety can be conveniently alkylated, thus allowing the insertion of functional groups, such a carboxylic acid, and enabling practical applications.

Chalcogen Bonding (ChB) as a Robust Supramolecular Recognition Motif of Benzisothiazolinone Antibacterials.

1,2-benzisothiazol-3(2H)-one derivatives are highly active against a broad spectrum of fungi as well as Gram positive and Gram negative bacteria. For this reason they are extensively used, for example, as additives in detergents, leather products, paper coatings, and antifouling paintings. In this paper experimental findings are reported proving that the sulfur atom of benzisothiazolinones have a remarkable tendency to form short and directional chalcogen bondings on the extension of the covalent N-S bond and, to a lesser extent, of the C-S bond. Analyses of the Cambridge Structural Database confirm the interaction as a primary recognition motif of these systems. The electrophilicity of sulfur is crucial in the chemical reactions initiating the cascade of events resulting in the biopharmacological activities of benzisothiazolinones. The reported results suggest that the electrophility of sulfur may play a role also at earlier stages than the reactive ones, namely it may pin the compounds at the active site of target enzymes via chalcogen bondings that preorganize the system in the conformation required for the bonds formation/cleavage determining the biopharmacological activity.

Tweaking the Optoelectronic Properties of S-Doped Polycyclic Aromatic Hydrocarbons by Chemical Oxidation.

Peri-thiaxanthenothiaxanthene, an S-doped analog of peri-xanthenoxanthene, is used as a polycyclic aromatic hydrocarbon (PAH) scaffold to tune the molecular semiconductor properties by editing the oxidation state of the S-atoms. Chemical oxidation of peri-thiaxanthenothiaxanthene with H2 O2 led to the relevant sulfoxide and sulfone congeners, whereas electrooxidation gave access to sulfonium-type derivatives forming crystalline mixed valence (MV) complexes. These complexes depicted peculiar molecular and solid-state arrangements with face-to-face π-π stacking organization. Photophysical studies showed a widening of the optical bandgap upon progressive oxidation of the S-atoms, with the bis-sulfone derivative displaying the largest value (E00 =2.99 eV). While peri-thiaxanthenothiaxanthene showed reversible oxidation properties, the sulfoxide and sulfone derivatives mainly showed reductive events, corroborating their n-type properties. Electric measurements of single crystals of the MV complexes exhibited a semiconducting behavior with a remarkably high conductivity at room temperature (10-1 -10-2  S cm-1 and 10-2 -10-3  S cm-1 for the O and S derivatives, respectively), one of the highest reported so far. Finally, the electroluminescence properties of the complexes were tested in light-emitting electrochemical cells (LECs), obtaining the first S-doped mid-emitting PAH-based LECs.

Computation meets experiment: identification of highly efficient fibrillating peptides.

Self-assembling peptides are of huge interest for biological, medical and nanotechnological applications. The enormous chemical variety that is available from the 20 amino acids offers potentially unlimited peptide sequences, but it is currently an issue to predict their supramolecular behavior in a reliable and cheap way. Herein we report a computational method to screen and forecast the aqueous self-assembly propensity of amyloidogenic pentapeptides. This method was found also as an interesting tool to predict peptide crystallinity, which may be of interest for the development of peptide based drugs.

Phenanthrene-Extended Phenazine Dication: An Electrochromic Conformational Switch Presenting Dual Reactivity.

The synthesis and isolation of one of the few examples of a π-extended diamagnetic phenazine dication have been achieved by oxidizing a phenanthrene-based dihydrophenazine precursor. The resulting dication was isolated and fully characterized, highlighting an aromatic distorted structure, generated by the conformational change upon the oxidation of the dihydrophenazine precursor, which is also correlated with a marked electrochromic change in the UV-vis spectrum. The aromaticity of the dication has also been investigated theoretically, proving that the species is aromatic based on all major criteria (structural, magnetic, and energetic). Moreover, the material presents an intriguing dual reactivity, resulting in ring contraction to a π-extended triarylimidazolinium and reduction to the dihydrophenazine precursor, depending on the nature of the nucleophile involved. This result helps shed light on the yet largely unexplored reactivity and properties of extended dicationic polycyclic aromatic hydrocarbons (PAHs). In particular, the fact that the molecule can undergo a reversible change in conformation upon oxidation and reduction opens potential applications for this class of derivatives as molecular switches and actuators.

peri-Acenoacene Ribbons with Zigzag BN-Doped Peripheries.

Here, we report the synthesis of BN-doped graphenoid nanoribbons, in which peripheral carbon atoms at the zigzag edges have been selectively replaced by boron and nitrogen atoms as BN and NBN motifs. This includes high-yielding ring closure key steps that, through N-directed borylation reaction using solely BBr3, allow the planarization of meta-oligoarylenyl precursors, through the formation of B-N and B-C bonds, to give ter-, quater-, quinque-, and sexi-arylenyl nanoribbons. X-ray single-crystal diffraction studies confirmed the formation of the BN and NBN motifs and the zigzag-edged topology of the regularly doped ribbons. Steady-state absorption and emission investigations at room temperature showed a systematic bathochromic shift of the UV-vis absorption and emission envelopes upon elongation of the oligoarylenyl backbone, with the nanoribbon emission featuring a TADF component. All derivatives displayed phosphorescence at 77 K. Electrochemical studies showed that the π-extension of the peri-acenoacene framework provokes a lowering of the first oxidative event (from 0.83 to 0.40 V), making these nanoribbons optimal candidates to engineer p-type organic semiconductors.

Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self-Assembly.

Iodination has long been employed as a successful labelling strategy to gain structural insights into proteins and other biomolecules via several techniques, including Small Angle X-ray Scattering, Inductively Coupled Plasma Mass Spectrometer (ICP-MS), and single-crystal crystallography. However, when dealing with smaller biomolecular systems, interactions driven by iodine may significantly alter their self-assembly behaviour. The engineering of amyloidogenic peptides for the development of ordered nanomaterials has greatly benefitted from this possibility. Still, to date, iodination has exclusively been applied to aromatic residues. In this work, an aliphatic bis-iodinated amino acid was synthesized and included into a custom pentapeptide, which showed enhanced fibrillogenic behaviour. Peptide single crystal X-ray structure and powder X-ray diffraction on its dried water solution demonstrated the key role of iodine atoms in promoting intermolecular interactions that drive the peptide self-assembly into amyloid fibrils. These findings enlarge the library of halogenated moieties available for directing and engineering the self-assembly of amyloidogenic peptides.

The Unexpected Helical Supramolecular Assembly of a Simple Achiral Acetamide Tecton Generates Selective Water Channels.

Invited for the cover of this issue is the collaborative research team coordinated by Arie van der Lee at the University of Montpellier. The image depicts chiral channels with highly mobile water molecules resulting from the robust self-organization of a simple achiral acetamide. Fully reversible release and re-uptake of water molecules takes place near ambient conditions, with efficient water transport and a good selectivity against NaCl suggesting it to be an efficient candidate for desalination processes. Read the full text of the article at 10.1002/chem.20200383.

The Unexpected Helical Supramolecular Assembly of a Simple Achiral Acetamide Tecton Generates Selective Water Channels.

Achiral 2-hydroxy-N-(diphenylmethyl)acetamide (HNDPA) crystallizes in the P61 chiral space group as a hydrate, building up permeable chiral crystalline helical water channels. The crystallization-driven chiral self-resolution process is highly robust, with the same air-stable crystalline form readily obtained under a variety of conditions. Interestingly, the HNDPA supramolecular helix inner pore is filled by a helical water wire. The whole edifice is mainly stabilized by robust hydrogen bonds involving the HNDPA amide bonds and CH… π interactions between the HNDPA phenyl groups. The crystalline structure shows breathing behavior, with completely reversible release and re-uptake of water inside the chiral channel under ambient conditions. Importantly, the HNDPA channel is able to transport water very efficiently and selectively under biomimetic conditions. With a permeability per channel of 3.3 million water molecules per second in large unilamellar vesicles (LUV) and total selectivity against NaCl, the HNDPA channel is a very promising functional nanomaterial for future applications.

Arabidopsis and Chlamydomonas phosphoribulokinase crystal structures complete the redox structural proteome of the Calvin-Benson cycle.

In land plants and algae, the Calvin-Benson (CB) cycle takes place in the chloroplast, a specialized organelle in which photosynthesis occurs. Thioredoxins (TRXs) are small ubiquitous proteins, known to harmonize the two stages of photosynthesis through a thiol-based mechanism. Among the 11 enzymes of the CB cycle, the TRX target phosphoribulokinase (PRK) has yet to be characterized at the atomic scale. To accomplish this goal, we determined the crystal structures of PRK from two model species: the green alga Chlamydomonas reinhardtii (CrPRK) and the land plant Arabidopsis thaliana (AtPRK). PRK is an elongated homodimer characterized by a large central ß-sheet of 18 strands, extending between two catalytic sites positioned at its edges. The electrostatic surface potential of the catalytic cavity has both a positive region suitable for binding the phosphate groups of substrates and an exposed negative region to attract positively charged TRX-f. In the catalytic cavity, the regulatory cysteines are 13 Å apart and connected by a flexible region exclusive to photosynthetic eukaryotes-the clamp loop-which is believed to be essential for oxidation-induced structural rearrangements. Structural comparisons with prokaryotic and evolutionarily older PRKs revealed that both AtPRK and CrPRK have a strongly reduced dimer interface and an increased number of random-coiled regions, suggesting that a general loss in structural rigidity correlates with gains in TRX sensitivity during the molecular evolution of PRKs in eukaryotes.

Folding Mechanism and Aggregation Propensity of the KH0 Domain of FMRP and Its R138Q Pathological Variant.

The K-homology (KH) domains are small, structurally conserved domains found in proteins of different origins characterized by a central conserved ßααß "core" and a GxxG motif in the loop between the two helices of the KH core. In the eukaryotic KHI type, additional αß elements decorate the "core" at the C-terminus. Proteins containing KH domains perform different functions and several diseases have been associated with mutations in these domains, including those in the fragile X mental retardation protein (FMRP). FMRP is an RNA-binding protein crucial for the control of RNA metabolism whose lack or mutations lead to fragile X syndrome (FXS). Among missense mutations, the R138Q substitution is in the KH0 degenerated domain lacking the classical GxxG motif. By combining equilibrium and kinetic experiments, we present a characterization of the folding mechanism of the KH0 domain from the FMRP wild-type and of the R138Q variant showing that in both cases the folding mechanism implies the accumulation of an on-pathway transient intermediate. Moreover, by exploiting a battery of biophysical techniques, we show that the KH0 domain has the propensity to form amyloid-like aggregates in mild conditions in vitro and that the R138Q mutation leads to a general destabilization of the protein and to an increased fibrillogenesis propensity.

Boosting Bismuth(III) Complexation for Targeted α-Therapy (TAT) Applications with the Mesocyclic Chelating Agent AAZTA.

Targeted α therapy (TAT) is a promising tool in the therapy of cancer. The radionuclide 213 BiIII shows favourable physical properties for this application, but the fast and stable chelation of this metal ion remains challenging. Herein, we demonstrate that the mesocyclic chelator AAZTA quickly coordinates BiIII at room temperature, leading to a robust complex. A comprehensive study of the structural, thermodynamic and kinetic properties of [Bi(AAZTA)]- is reported, along with bifunctional [Bi(AAZTA-C4-COO- )]2- and the targeted agent [Bi(AAZTA-C4-TATE)]- , which incorporates the SSR agonist Tyr3 -octreotate. An unexpected increase in the stability and kinetic inertness of the metal chelate was observed for the bifunctional derivative and was maintained for the peptide conjugate. A cyclotron-produced 205/206 Bi mixture was used as a model of 213 Bi in labelling, stability, and biodistribution experiments, allowing the efficiency of [213 Bi(AAZTA-C4-TATE)]- to be estimated. High accumulation in AR42J tumours and reduced kidney uptake were observed with respect to the macrocyclic chelate [213 Bi(DOTA-TATE)]- .

Photoinduced Electron vs. Concerted Proton Electron Transfer Pathways in SnIV (l-Tryptophanato)2 Porphyrin Conjugates.

Aromatic amino acids such as l-tyrosine and l-tryptophan are deployed in natural systems to mediate electron transfer (ET) reactions. While tyrosine oxidation is always coupled to deprotonation (proton-coupled electron-transfer, PCET), both ET-only and PCET pathways can occur in the case of the tryptophan residue. In the present work, two novel conjugates 1 and 2, based on a SnIV tetraphenylporphyrin and SnIV octaethylporphyrin, respectively, as the chromophore/electron acceptor and l-tryptophan as electron/proton donor, have been prepared and thoroughly characterized by a combination of different techniques including single crystal X-ray analysis. The photophysical investigation of 1 and 2 in CH2 Cl2 in the presence of pyrrolidine as a base shows that different quenching mechanisms are operating upon visible-light excitation of the porphyrin component, namely photoinduced electron transfer and concerted proton electron transfer (CPET), depending on the chromophore identity and spin multiplicity of the excited state. The results are compared with those previously described for metal-mediated analogues featuring SnIV porphyrin chromophores and l-tyrosine as the redox active amino acid and well illustrate the peculiar role of l-tryptophan with respect to PCET.

Giant Shape-Persistent Tetrahedral Porphyrin System: Light-Induced Charge Separation.

Tetraphenylmethane appended with four pyridylpyridinium units works as a scaffold to self-assemble four ruthenium porphyrins in a tetrahedral shape-persistent giant architecture. The resulting supramolecular structure has been characterised in the solid state by X-ray single crystal analysis and in solution by various techniques. Multinuclear NMR spectroscopy confirms the 1 : 4 stoichiometry with the formation of a highly symmetric structure. The self-assembly process can be monitored by changes of the redox potentials, as well as by modifications in the visible absorption spectrum of the ruthenium porphyrin and by a complete quenching of both the bright fluorescence of the tetracationic scaffold and the weak phosphorescence of the ruthenium porphyrin. An ultrafast photoinduced electron transfer is responsible for this quenching process. The lifetime of the resulting charge separated state (800 ps) is about four times longer in the giant supramolecular structure compared to the model 1 : 1 complex formed by the ruthenium porphyrin and a single pyridylpyridinium unit. Electron delocalization over the tetrameric pyridinium structure is likely to be responsible for this effect.

BN-Doped Metal-Organic Frameworks: Tailoring 2D and 3D Porous Architectures through Molecular Editing of Borazines.

Building on the MOF approach to prepare porous materials, herein we report the engineering of porous BN-doped materials using tricarboxylic hexaarylborazine ligands, which are laterally decorated with functional groups at the full-carbon 'inner shell'. Whilst an open porous 3D entangled structure could be obtained from the double interpenetration of two identical metal frameworks derived from the methyl substituted borazine, the chlorine-functionalised linker undergoes formation of a porous layered 2D honeycomb structure, as shown by single-crystal X-ray diffraction analysis. In this architecture, the borazine cores are rotated by 60° in alternating layers, thus generating large rhombohedral channels running perpendicular to the planes of the networks. An analogous unsubstituted full-carbon metal framework was synthesised for comparison. The resulting MOF revealed a crystalline 3D entangled porous structure, composed by three mutually interpenetrating networks, hence denser than those obtained from the borazine linkers. Their microporosity and CO2 uptake were investigated, with the porous 3D BN-MOF entangled structure exhibiting a large apparent BET specific surface area (1091 m2 g-1 ) and significant CO2 reversible adsorption (3.31 mmol g-1 ) at 1 bar and 273 K.

Underlining the Importance of Peripheral Protic Functional Groups to Enhance the Proton Exchange of Gd-Based MRI Contrast Agents.

In this study, we report the synthesis and the equilibrium, kinetic, relaxation, and structural properties of two new GdIII complexes based on modified 10-(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (HPDO3A) designed to modulate the relaxivity at acidic and basic pH due to intra- and intermolecular proton exchange. The presence of a carboxylic or ester moieties in place of the methyl group of HPDO3A allowed differentiation of a protic and nonprotic functional group, highlighting the importance of the formation of an intramolecular hydrogen bond between the coordinated hydroxyl and the carboxylate groups for proton exchange (kH = 1.5 × 1011 M-1 s-1, kOH = 1.7 × 109 M-1 s-1). The determination of the thermodynamic stability and kinetic inertness of the GdIII complexes confirmed that the modification of peripheral groups does not significantly affect the coordination environment and thus the stability (log KGdL = 19.26, t1/2 = 2.14 × 107 hours, pH = 7.4, 0.15 M NaCl, 25 °C). The relaxivity (r1) was measured as a function of pH to investigate the proton exchange kinetics, and as a function of the magnetic field strength to extrapolate the relaxometric parameters (r1GdL1 = 4.7 mM-1 s-1 and r1GdL2 = 5.1 mM-1 s-1 at 20 MHz, 25 °C, and pH 7.4). Finally, the X-ray crystal structure of the complex crystallized at basic pH showed the formation of a tetranuclear dimer with alkoxide and hydroxide groups bridging the GdIII ions.

Spectroscopic/Computational Characterization and the X-ray Structure of the Adduct of the VIVO-Picolinato Complex with RNase A.

The structure, stability, and enzymatic activity of the adduct formed upon the reaction of the V-picolinato (pic) complex [VIVO(pic)2(H2O)], with an octahedral geometry and the water ligand in cis to the V═O group, with the bovine pancreatic ribonuclease (RNase A) were studied. While electrospray ionization-mass spectrometry, circular dichroism, and ultraviolet-visible absorption spectroscopy substantiate the interaction between the metal moiety and RNase A, electron paramagnetic resonance (EPR) allows us to determine that a carboxylate group, stemming from Asp or Glu residues, and imidazole nitrogen from His residues are involved in the V binding at acidic and physiological pH, respectively. Crystallographic data demonstrate that the VIVO(pic)2 moiety coordinates the side chain of Glu111 of RNase A, by substituting the equatorial water molecule at acidic pH. Computational methods confirm that Glu111 is the most affine residue and interacts favorably with the OC-6-23-Δ enantiomer establishing an extended network of hydrogen bonds and van der Waals stabilizations. By increasing the pH around neutrality, with the deprotonation of histidine side chains, the binding of the V complex to His105 and His119 could occur, with that to His105 which should be preferred when compared to that to the catalytically important His119. The binding of the V compound affects the enzymatic activity of RNase A, but it does not alter its overall structure and stability.