Aminoquinoline-Based Tridentate (NNN)-Copper Catalyst for C-N Bond-Forming Reactions from Aniline and Diazo Compounds.

A new tridentate Cu2+ complex based on (E)-1-(pyridin-2-yl)-N-(quinolin-8-yl)methanimine (PQM) was generated and characterized to support the activation of diazo compounds for the formation of new C-N bonds. This neutral Schiff base ligand was structurally characterized to coordinate with copper(II) in an equatorial fashion, yielding a distorted octahedral complex. Upon characterization, this copper(II) complex was used to catalyze an efficient and cost-effective protocol for C-N bond formation between N-nucleophiles and copper carbene complexes arising from the activation of diazo carbonyl compounds. A substrate scope of approximately 15 different amine-based substrates was screened, yielding 2° or 3° amine products with acceptable to good yields under mild reaction conditions. Reactivity towards phenol and thiophenol were also screened, showing relatively weak C-O or C-S bond formation under optimized conditions.

Three water-soluble copper(II) N-heterocyclic carbene complexes: toward copper-catalyzed ketone reduction under sustainable conditions.

A series of tridentate copper(II) N-heterocyclic carbene (NHC) complexes with imidazole, benzimidazole, and 5,6-dimethylbenzimidazole azole rings were synthesized and comprehensively characterized via X-ray crystallography, ESI-MS, cyclic voltammetry, and UV-Vis and EPR spectroscopic studies. These complexes were then utilized for the optimization of ketone reduction under sustainable conditions using 2-acetylpyridine and phenylsilane. The relationships between product formation, temperature, reaction time, and catalyst loading for the hydrogenation reactions are covered in detail. Reduction of eighteen different aliphatic, cyclic, and aromatic ketones were demonstrated, which were compatible to produce the corresponding products in moderate to good yields. These systems were used to develop related DNA-hybrid catalytic systems, but only supported weak enantioselectivity. Further thermodynamic experiments showed Cu-NHC complexes did not demonstrate specific binding to DNA, which is consistent with their limited selectivity.

Copper complexes for the chemoselective N-arylation of arylamines and sulfanilamides via Chan-Evans-Lam cross-coupling.

Copper(II) complexes with tridentate NNN-ligands were utilized for Chan-Evans-Lam (CEL) cross-coupling reactions to enable the N-arylation of multifarious N-nucleophiles through the activation of aryl boronic acids. A condition-specific methodology was developed to chemoselectively target the amine versus sulfonamide N-arylation of 4-aminobenzenesulfonamide using new catalysts. Two different pyridine-based ligands and corresponding copper(II) complexes were characterized using 1H and 13C-NMR, FTIR, and UV-vis spectroscopy, HRMS, single-crystal X-ray diffraction, and cyclic voltammetry. Solvent and base-controlled cross-coupling reactions were observed, which led to the optimization of selective conditions for targeted C-N bond formation of sulfanilamides. Beyond the chemoselective processes reported here, a breadth of N-nucleophiles including sulfanilamides and arylamines were screened for arylation by this CEL catalyst.

Sodium Trifluoroacetate mediated Copper-Catalyzed aza-Michael addition of α,ß-unsaturated olefins with aromatic amines.

We present a sodium trifluoroacetate (CF3CO2Na) mediated copper-catalyzed aza-Michael addition of aromatic amines with activated olefins under mild, aqueous reaction conditions. This simplistic protocol employs a copper catalyst (10 mol%) and water as solvent. This transformation occurs precisely with aromatic substituted amines containing both electron-donating (EDG) and electron-withdrawing (EWG) groups. A broad range of substrates were tested under the optimized conditions, which are producing good to moderate yields.

Pre-mRNA splicing-associated diseases and therapies.

Precursor mRNA (pre-mRNA) splicing is an essential step in human gene expression and is carried out by a large macromolecular machine called the spliceosome. Given the spliceosome's role in shaping the cellular transcriptome, it is not surprising that mutations in the splicing machinery can result in a range of human diseases and disorders (spliceosomopathies). This review serves as an introduction into the main features of the pre-mRNA splicing machinery in humans and how changes in the function of its components can lead to diseases ranging from blindness to cancers. Recently, several drugs have been developed that interact directly with this machinery to change splicing outcomes at either the single gene or transcriptome-scale. We discuss the mechanism of action of several drugs that perturb splicing in unique ways. Finally, we speculate on what the future may hold in the emerging area of spliceosomopathies and spliceosome-targeted treatments.

Calorimetric analysis of AdcR and its interactions with zinc(II) and DNA.

Zinc(II) ions play critical roles in all known life as structurally important stabilizing ions in proteins, catalytically active metals in enzymes, and signaling agents impacting physiological changes. To maintain homeostasis, the intracellular concentration of zinc(II) is strictly controlled by a family of metal-regulatory proteins in both prokaryotic and eukaryotic organisms. In S. pneumoniae, there are two proteins that share responsibility for Zn2+ homeostasis, one of them is the Adhesin Competence Repressor (AdcR) and it binds to a specific double-stranded DNA binding domain (dsDNA). AdcR has been structurally characterized containing two zinc(II) metal centers per monomeric unit. Here we report data collected from differential scanning calorimetry (DSC) experiments aimed to measure the structural stability of AdcR, the fully complimented Zn2AdcR complex, and the protein/DNA complex Zn2AdcR/dsDNA. Thermograms collected from DSC experiments yielded endothermic unfolding events for AdcR, Zn2AdcR, and Zn2AdcR/dsDNA complex at 55.6, 70.2, and 56.6 °C, respectively. A non-two state unfolding model best fits the data, giving ΔH terms associated with these thermal unfolding events of 5.1, 7.1, and 4.9 kcal/mol. These data allow for the development of a thermodynamic cycle connecting both zinc(II) and DNA binding to AdcR. Furthermore, pairing this newly reported data with known association constants for zinc(II) and DNA binding allowed for the generation of thermodynamic profiles for both zinc(II) binding to AdcR and Zn2AdcR binding to DNA, which show both are decisively entropy-driven processes.

Improved Synthesis of the Amine Fragment of FR901464 and Thailanstatins through the Development of a Convenient N-Detosylation Method.

FR901464 and thailanstatins are potent cytotoxic natural products that share an amine-containing tetrahydropyran ring. We previously reported the synthesis of the tetrahydropyran component. Here, we changed the protecting group for the amine from Boc to tosyl, improving yields and the time economy. A highlight of the revised synthetic scheme is the use of lithium, t-butanol, and ethylenediamine in THF (nontraditional Birch reduction conditions) for the N-detosylation.

Thermodynamics of iron, tetrahydrobiopterin, and phenylalanine binding to phenylalanine hydroxylase from Chromobacterium violaceum.

Phenylalanine hydroxylase (PheH) is a pterin-dependent, mononuclear nonheme iron(II) oxygenase that uses the oxidative power of O2 to hydroxylate phenylalanine to form tyrosine. PheH is a member of a superfamily of O2-activating enzymes that utilizes a common metal binding motif: the 2-His-1-carboxylate facial triad. Like most members of this superfamily, binding of substrates to PheH results in a reorganization of its active site to allow O2 activation. Exploring the energetics of each step before O2 activation can provide mechanistic insight into the initial steps that support the highly specific O2 activation pathway carried out by this metalloenzyme. Here the thermal stability of PheH and its substrate complexes were investigated under an anaerobic environment by using differential scanning calorimetry. In context with known binding constants for PheH, a thermodynamic cycle associated with iron(II), tetrahydrobiopterin (BH4), and phenylalanine binding to the active site was generated, showing a distinctive cooperativity between the binding of BH4 and Phe. The addition of phenylalanine and BH4 to PheH·Fe increased the stability of this enzyme (ΔTm of 8.5 (±0.7) °C with an associated δΔH of 43.0 (±2.9) kcal/mol). The thermodynamic data presented here gives insight into the complicated interactions between metal center, cofactor, and substrate, and how this interplay sets the stage for highly specific, oxidative C-H activation in this enzyme.

Cu-Catalyzed Chan-Evans-Lam Coupling Reactions of 2-Nitroimidazole with Aryl Boronic Acids: An Effort toward New Bioactive Agents against S.†pneumoniae.

The coupling of phenylboronic acids with poorly-activated imidazoles is studied as a model system to explore the use of copper-catalyzed Chan-Evans-Lam (CEL) coupling for targeted C-N bond forming reactions. Optimized CEL reaction conditions are reported for four phenanthroline-based ligand systems, where the ligand 4,5-diazafluoren-9-one (dafo, L2) with 1 molar equivalent of potassium carbonate yielded the highest reactivity. The substrate 2-nitroimidazole (also known as azomycin) has documented antimicrobial activity against a range of microbes. Here N-arylation of 2-nitroimidazole with a range of aryl boronic acids has been successfully developed by copper(II)-catalyzed CEL reactions. Azomycin and a range of newly arylated azomycin derivatives were screened against S. pneumoniae, where 1-(4-(benzyloxy)phenyl)-2-nitro-1H-imidazole (3d) was demonstrated to have a minimal inhibition concentration value of 3.3 µg/mL.

Metal Ion Binding Induces Local Protein Unfolding and Destabilizes Human Carbonic Anhydrase II.

Human carbonic anhydrase II (HCA) is a robust metalloprotein and an excellent biological model system to study the thermodynamics of metal ion coordination. Apo-HCA binds one zinc ion or two copper ions. We studied these binding processes at five temperatures (15-35 °C) using isothermal titration calorimetry, yielding thermodynamic parameters corrected for pH and buffer effects. We then sought to identify binding-induced structural changes. Our data suggest that binding at the active site organizes 6-8 residues; however, copper binding near the N-terminus results in a net unfolding of 6-7 residues. This surprising destabilization was confirmed using circular dichroism and protein stability measurements. Metal binding induced unfolding may represent an important regulatory mechanism, but it may be easily missed by NMR and X-ray crystallography. Thus, in addition to highlighting a highly novel binding-induced unfolding event, we demonstrate the value of calorimetry for studying the structural implications of metal binding.

Copper(II) NHC Catalyst for the Formation of Phenol from Arylboronic Acid.

Arylboronic acids are commonly used in modern organic chemistry to form new C-C and C-heteroatom bonds. These activated organic synthons show reactivity with heteroatoms in a range of substrates under ambient oxidative conditions. This broad reactivity has limited their use in protic, renewable solvents like water, ethanol, and methanol. Here, we report our efforts to study and optimize the activation of arylboronic acids by a copper(II) N-heterocyclic carbene (NHC) complex in aqueous solution and in a range of alcohols to generate phenol and aryl ethers, respectively. The optimized reactivity showcases the ability to make targeted C-O bonds, but also identifies conditions where water and alcohol activation could be limiting for C-C and C-heteroatom bond-forming reactions. This copper(II) complex shows strong reactivity toward arylboronic acid activation in aqueous medium at ambient temperature. The relationship between product formation and temperature and catalyst loading are described. Additionally, the effects of buffer, pH, base, and co-solvent are explored with respect to phenol and ether generation reactions. Characterization of the new copper(II) NCN-pincer complex by X-ray crystallography, HR-MS, cyclic voltammetry, FT-IR and UV-Vis spectral studies is reported.

Simulating and Mitigating Crosstalk.

We describe an efficient and scalable framework for modeling crosstalk effects on quantum information processors. By applying optimal control techniques, we show how to tune-up arbitrary high-fidelity parallel operations on systems with substantial local and nonlocal crosstalk. As an example, we simulate a 2D square array of 100 superconducting transmon qubits. These results suggest that rather than striving to engineer away undesirable interactions during fabrication, we can largely mitigate such effects with software through careful characterization and control optimization.

Multivariate data analysis in cell gene therapy manufacturing.

The emergence of cell gene therapy (CGT) as a safe and efficacious treatment for numerous severe inherited and acquired human diseases has led to growing interest and investment in new CGT products. The most successful of these have been autologous viral vector-based treatments. The development of viral vector manufacturing processes and ex vivo patient cell processing capabilities is a pressing issue in the advancement of autologous viral vector-based CGT treatments. In viral vector production, scale-up is a critical task due to the limited scalability of traditional laboratory systems and the demand for high volumes of viral vector manufactured in accordance with current good manufacturing practice. Ex vivo cell processing methods require optimisation and automation before they can be scaled out, and several other manufacturing challenges are prevalent such as high levels of raw material and process variability, difficulty characterising complex materials, and a lack of knowledge of critical process parameters and their effect on critical quality attributes of the viral vector and cell drug products. Multivariate data analysis (MVDA) has been leveraged successfully in a variety of applications in the chemical and biochemical industries, including for tasks such as bioprocess monitoring, identification of critical process parameters and assessment of process variability and comparability during process development, scale-up and technology transfer. Henceforth, MVDA is reviewed here as a suitable tool for tackling some of the challenges faced in the development of CGT manufacturing processes. A summary of some key CGT manufacturing challenges is provided along with a review of MVDA applications to mammalian and microbial processes, and an exploration of the potential benefits, requirements and pre-requisites of MVDA applications in the development of CGT manufacturing processes.

Streptococcus pneumoniae metal homeostasis alters cellular metabolism.

Streptococcus pneumoniae colonizes the human nasopharyngeal mucosa and is a leading cause of community-acquired pneumonia, acute otitis media, and bacterial meningitis. Metal ion homeostasis is vital to the survival of this pathogen across diverse biological sites and contributes significantly to colonization and invasive disease. Microarray and qRT-PCR analysis revealed an upregulation of an uncharacterized operon (SP1433-1438) in pneumococci subjected to metal-chelation by N,N,N',N'-tetrakis-(2-pyridylmethyl)ethylenediamine (TPEN). Supplementation of zinc, cobalt, and nickel following TPEN treatment significantly abrogated induction. BLASTP comparisons and protein topology analysis predicted this locus to encode components of ATP binding cassette (ABC) transporters involved in multidrug resistance (SP1434-1435) and energy-coupling factor (ECF) transporters (SP1436-1438). Inductively coupled plasma mass spectrometry (ICP-MS) analysis identified differences in intracellular metal content in a Δ1434-8 mutant strain compared to parental T4R. Further, analysis of the secreted metabolome of WT and Δ1434-8 strains identified significant changes in pneumococcal glycolytic and amino acid metabolic pathways, indicating a shift towards mixed acid fermentation. Additionally, proteomic analysis revealed differentially expressed proteins in the Δ1434-8 mutant strain, with nearly 20% regulated by the global catabolite repressor, CcpA. Based on these findings, we propose that the transporters encoded by SP1433-1438 are involved in regulating the central metabolism of S. pneumoniae and contributing to bacterial survival during metal stress.

Tuning the copper(II)/copper(I) redox potential for more robust copper-catalyzed C-N bond forming reactions.

Complexes of copper and 1,10-phenanthroline have been utilized for organic transformations over the last 50 years. In many cases these systems are impacted by reaction conditions and perform best under an inert atmosphere. Here we explore the role the 1,10-phenanthroline ligand plays on the electronic structure and redox properties of copper coordination complexes, and what benefit related ligands may provide to enhance copper-based coupling reactions. Copper(II) triflate complexes bearing 1,10-phenanthroline (phen), ([Cu(phen)2(OTf)]OTf, 1) and oxidized derivatives of phen including [Cu(edhp)2](OTf)2 (2), [Cu(pdo)2](OTf)2 (3), [Cu(dafo)2](OTf)2 (4) were prepared and characterized. X-ray crystallographic data show these related ligands subtly impacted the coordination geometry of the copper(II) ion. Complexes 1-3 had only incremental changes to the redox properties of the copper ions, complex 4 showed a drastically different redox potential affording a remarkably air stable copper(I) complex. These complexes 1-4 were then used to catalyze the C-N bond forming cross coupling between imidazole and various boronic acid substrates, where the increased stability of the copper(I) species in complex 4 appears to better support these CEL cross couplings.

Characterizing large-scale quantum computers via cycle benchmarking.

Quantum computers promise to solve certain problems more efficiently than their digital counterparts. A major challenge towards practically useful quantum computing is characterizing and reducing the various errors that accumulate during an algorithm running on large-scale processors. Current characterization techniques are unable to adequately account for the exponentially large set of potential errors, including cross-talk and other correlated noise sources. Here we develop cycle benchmarking, a rigorous and practically scalable protocol for characterizing local and global errors across multi-qubit quantum processors. We experimentally demonstrate its practicality by quantifying such errors in non-entangling and entangling operations on an ion-trap quantum computer with up to 10 qubits, and total process fidelities for multi-qubit entangling gates ranging from [Formula: see text] for 2 qubits to [Formula: see text] for 10 qubits. Furthermore, cycle benchmarking data validates that the error rate per single-qubit gate and per two-qubit coupling does not increase with increasing system size.

Contextuality and the Single-Qubit Stabilizer Subtheory.

Contextuality is a fundamental nonclassical property of quantum theory, which has recently been proven to be a key resource for achieving quantum speed-ups in some leading models of quantum computation. However, which of the forms of contextuality, and how much thereof, are required to obtain a speed-up in an arbitrary model of quantum computation remains unclear. In this Letter, we show that the relation between contextuality and a computational advantage is more complicated than previously thought. We achieve this by proving that generalized contextuality is present even within the simplest subset of quantum operations, the so-called single-qubit stabilizer theory, which offers no computational advantage and was previously believed to be completely noncontextual. However, the contextuality of the single-qubit stabilizer theory can be confined to transformations. Therefore, our result also demonstrates that the commonly considered prepare-and-measure scenarios (which ignore transformations) do not fully capture the contextuality of quantum theory.

Thermodynamics of Iron(II) and Substrate Binding to the Ethylene-Forming Enzyme.

The ethylene-forming enzyme (EFE), like many other 2-oxoglutarate (2OG)-dependent nonheme iron(II) oxygenases, catalyzes the oxidative decarboxylation of 2OG to succinate and CO2 to generate a highly reactive iron species that hydroxylates a specific alkane C-H bond, in this case targeting l-arginine (Arg) for hydroxylation. However, the prominently observed reactivity of EFE is the transformation of 2OG into ethylene and three molecules of CO2. Crystallographic and biochemical studies have led to several proposed mechanisms for this 2-fold reactivity, but the detailed reaction steps are still obscure. Here, the thermodynamics associated with iron(II), 2OG, and Arg binding to EFE are studied using calorimetry (isothermal titration calorimetry and differential scanning calorimetry) to gain insight into how these binding equilibria organize the active site of EFE, which may have an impact on the O2 activation pathways observed in this system. Calorimetric data show that the addition of iron(II), Arg, and 2OG increases the stability over that of the apoenzyme, and there is distinctive cooperativity between substrate and cofactor binding. The energetics of binding of 2OG to Fe·EFE are consistent with a unique monodentate binding mode, which is different than the prototypical 2OG coordination mode in other 2OG-dependent oxygenases. This difference in the pre-O2 activation equilibria may be important for supporting the alternative ethylene-forming chemistry of EFE.

The Irving-Williams series and the 2-His-1-carboxylate facial triad: a thermodynamic study of Mn2+, Fe2+, and Co2+ binding to taurine/α-ketoglutarate dioxygenase (TauD).

Taurine/α-ketoglutarate (αKG) dioxygenase (TauD) is an E. coli nonheme Fe2+- and αKG-dependent metalloenzyme that catalyzes the hydroxylation of taurine, leading to the production of sulfite. The metal-dependent active site in TauD is formed by two histidine and one aspartate that coordinating to one face of an octahedral coordination geometry, known as the 2-His-1-carboxylate facial triad. This motif is found in many nonheme Fe2+ proteins, but there is limited information on the thermodynamic parameters that govern metal-ion binding to this site. Here, we report data from calorimetry and related biophysical techniques to generate complete thermodynamic profiles of Mn2+ and Co2+ binding to TauD, and these values are compared to the Fe2+ data reported earlier Henderson et al. (Inorg Chem 54: 2278-2283, 2015). The buffer-independent binding constants (K) were measured to be 1.6 × 106, 2.4 × 107, and 1.7 × 109, for Mn2+, Fe2+, and Co2+, respectively. The corresponding ΔG° values were calculated to be - 8.4, - 10.1, and - 12.5 kcal/mol, respectively. The metal-binding enthalpy changes (ΔH) for these binding events are - 11.1 (± 0.1), - 12.2 (± 0.1), and - 16.0 (± 0.6) kcal/mol, respectively. These data are fully consistent with the Irving-Williams series, which show an increasing affinity for transition metal ions across the periodic table. It appears that the periodic increase in affinity, however, is a result of a complicated summation of enthalpy terms (including favorable metal-ion coordination processes and unfavorable ionization events) and related entropy terms.

Resolving distinct molecular origins for copper effects on PAI-1.

Components of the fibrinolytic system are subjected to stringent control to maintain proper hemostasis. Central to this regulation is the serpin plasminogen activator inhibitor-1 (PAI-1), which is responsible for specific and rapid inhibition of fibrinolytic proteases. Active PAI-1 is inherently unstable and readily converts to a latent, inactive form. The binding of vitronectin and other ligands influences stability of active PAI-1. Our laboratory recently observed reciprocal effects on the stability of active PAI-1 in the presence of transition metals, such as copper, depending on the whether vitronectin was also present (Thompson et al. Protein Sci 20:353-365, 2011). To better understand the molecular basis for these copper effects on PAI-1, we have developed a gel-based copper sensitivity assay that can be used to assess the copper concentrations that accelerate the conversion of active PAI-1 to a latent form. The copper sensitivity of wild-type PAI-1 was compared with variants lacking N-terminal histidine residues hypothesized to be involved in copper binding. In these PAI-1 variants, we observed significant differences in copper sensitivity, and these data were corroborated by latency conversion kinetics and thermodynamics of copper binding by isothermal titration calorimetry. These studies identified a copper-binding site involving histidines at positions 2 and 3 that confers a remarkable stabilization of PAI-1 beyond what is observed with vitronectin alone. A second site, independent from the two histidines, binds metal and increases the rate of the latency conversion.