Structural and Functional Aspects of Metal Sites in Biology

Identification of novel yolk ferritins unique to planarians: planarians supply aluminum rather than iron to vitellaria in egg capsules

All animals, other than Platyhelminthes, produce eggs containing yolk, referred to as "entolecithal" eggs. However, only Neoophora, in the phylum Platyhelminthes, produce "ectolecithal" eggs (egg capsules), in which yolk is stored in the vitelline cells surrounding oocytes. Vitelline cells are derived from vitellaria (yolk glands). Vitellaria are important reproductive organs that may be studied to elucidate unique mechanisms that have been evolutionarily conserved within Platyhelminthes. Currently, only limited molecular level information is available on vitellaria. The current study identified major vitellaria-specific proteins in a freshwater planarian, Dugesia ryukyuensis, using peptide mass fingerprinting (PMF) and expression analyses. Amino acid sequence analysis and orthology analysis via OrthoFinder ver.2.3.8 indicated that the identified major vitellaria-specific novel yolk ferritins were conserved in planarians (Tricladida). Because ferritins play an important role in Fe (iron) storage, we examined the metal elements contained in vitellaria and ectolecithal eggs, using non-heme iron histochemistry, elemental analysis based on inductively coupled plasma mass spectrometry and transmission electron microscopy- energy-dispersive X-ray spectroscopy analysis. Interestingly, vitellaria and egg capsules contained large amounts of aluminum (Al), but not Fe. The knockdown of the yolk ferritin genes caused a decrease in the volume of egg capsules, abnormality in juveniles, and increase in Al content in vitellaria. Yolk ferritins of D. ryukyuensis may regulate Al concentration in vitellaria via their pooling function of Al and protect the egg capsule production and normal embryogenesis from Al toxicity.

Accelerated Redox Reaction of Hydrogen Peroxide by Employing Locally Concentrated State of Copper Catalysts on Polymer Chain

Copper complexes act as catalysts for redox reactions to generate reactive oxygen species that destroy biomolecules and, therefore, are utilized to design drugs including antitumor and antibacterial medicines. Especially, catalytic reaction for hydrogen peroxide decomposition is important because it includes the process for generating highly toxic hydroxyl radical, i.e., Fenton-like reaction. Considering that multicoppers/hydrogen peroxide species are the important intermediates for the redox reaction, herein a polymer having copper complexes in the side chains is designed to facilitate the formation of the intermediates by building locally concentrated state of the copper complexes. The polymer increases their catalytic activities for hydrogen peroxide decomposition and promotes reactive oxygen species' generation, eventually leading to higher antibacterial activity. This reveals the virtue of building a locally concentrated state of catalysts on polymers toward drug design with low amounts of transition metals.

Electronic Structure of Tetrahedral, S = 2, [Fe{(EPiPr2)2N}2], E = S, Se, Complexes: Investigation by High-Frequency and -Field Electron Paramagnetic Resonance, 57Fe Mössbauer Spectroscopy, and Quantum Chemical Studies

In this work, we assessed the electronic structures of two pseudotetrahedral complexes of FeII, [Fe{(SPiPr2)2N}2] (1) and [Fe{(SePiPr2)2N}2] (2), using high-frequency and -field EPR (HFEPR) and field-dependent 57Fe Mössbauer spectroscopies. This investigation revealed S = 2 ground states characterized by moderate, negative zero-field splitting (zfs) parameters D. The crystal-field (CF) theory analysis of the spin Hamiltonian (sH) and hyperfine structure parameters revealed that the orbital ground states of 1 and 2 have a predominant dx2-y2 character, which is admixed with dz2 (∼10%). Although replacing the S-containing ligands of 1 by their Se-containing analogues in 2 leads to a smaller |D| value, our theoretical analysis, which relied on extensive ab initio CASSCF calculations, suggests that the ligand spin-orbit coupling (SOC) plays a marginal role in determining the magnetic anisotropy of these compounds. Instead, the dx2-y2β → dxyβ excitations yield a large negative contribution, which dominates the zfs of both 1 and 2, while the different energies of the dx2-y2β → dxzβ transitions are the predominant factor responsible for the difference in zfs between 1 and 2. The electronic structures of these compounds are contrasted with those of other [FeS4] sites, including reduced rubredoxin by considering a D2-type distortion of the [Fe(E-X)4] cores, where E = S, Se; X = C, P. Our combined CASSCF/DFT calculations indicate that while the character of the orbital ground state and the quintet excited states' contribution to the zfs of 1 and 2 are modulated by the magnitude of the D2 distortion, this structural change does not impact the contribution of the excited triplet states.

Synthesis and spectroscopic interpretations of Co(II), Ni(II) and Cu(II) decxycholate complexes with molecular docking of COVId-19 protease

Co(II), Ni(II) and Cu(II) decxycholate complexes are interesting due to their biologically active and deliberate interest in the research due to their coordination properties. The microanalytical ‘elemental analysis’, molar conductivity, (infrared and Raman) spectroscopy, thermal analyses (TGA/DSC), UV-vis spectra, and ESR for copper(II) decxycholate complex investigations were performed in the structural assignments of Co(II), Ni(II) and Cu(II) decxycholate complexes. Reaction of the sodium deoxycholate ligand (C24H39O4Na) with three transition metal ions form the complexes of formulae, [M(C24H39O4)2(H2O)2]. xH2O where M = Co(II), Ni(II) and Cu(II) where x = 2 for Cu(II) and x = 4 in case of M = Co(II) or Ni(II) metal ions. The FTIR spectra of the complexes show that decxycholate molecule is present as bidentate ligand. Molecular docking utilizing to additionally examine the interaction of COVID-19 (6LU7) with different complexes of deoxycholic acid with Co(II), Ni(II) and Cu(II). Furthermore, in the case of Co(II) deoxycholate complex, the probe is surrounded by amino residues Met235, Pro241, Glu240, Pro108, Gln110, Phe294, and Ile152. The probe molecule of Ni(II) deoxycholate complex is sited close to amino acids Tyr126, Tyr239, Leu287, Leu272, and Lys137. For, Cu(II) deoxycholate complex, the residues of amino acids comprise of Pro132, Pro108, Gln110, Gly109, Ile200, Asn203, Val202, His246, Pro293 and Tyr154. The binding energy was determined from the docking reads for Co(II)–6LU7, Ni(II)–6LU7 and Cu(II)–6LU7 deoxycholate compounds were found to be −446.99, −500.52, −398.13 kcal mol−1 individually.

Rotaxane CoII Complexes as Field-Induced Single-Ion Magnets

Mechanically chelating ligands have untapped potential for the engineering of metal ion properties. Here we demonstrate this principle in the context of CoII -based single-ion magnets. Using multi-frequency EPR, susceptibility and magnetization measurements we found that these complexes show some of the highest zero field splittings reported for five-coordinate CoII complexes to date. The predictable coordination behaviour of the interlocked ligands allowed the magnetic properties of their CoII complexes to be evaluated computationally a priori and our combined experimental and theoretical approach enabled us to rationalize the observed trends. The predictable magnetic behaviour of the rotaxane CoII complexes demonstrates that interlocked ligands offer a new strategy to design metal complexes with interesting functionality.

Metal-ion promiscuity of microbial enzyme DapE at its second metal-binding site

Metalloenzymes are ubiquitous in nature catalyzing a number of crucial biochemical processes in animal and plant kingdoms. For better adaptation to the relative abundance of different metal ions in different cellular fluids, many of these enzymes exhibit metal promiscuity. The microbial enzyme DapE, an essential enzyme for bacterial growth and survival and a potentially safe target for antibiotics, continues to show enzyme activity when the two zinc ions in its active site are replaced by other transition metal ions. The effect of metal-ion substitution at the second metal-binding site of DapE on its substrate affinity and catalytic efficiency is investigated by QM/MM treatment of the enzyme-substrate complex, by modelling the enzyme with Mn(II), Co(II), Ni(II), or Cu(II) ion in place of Zn(II) at its second metal-binding site, while retaining Zn(II) ion at the first metal-binding site. On the basis of substrate binding energy and activation energy barrier for the chemical catalysis, it is found that Zn-Mn DapE shows poor binding affinity as well as inefficient chemical catalysis. Although Zn-Cu and Zn-Ni DapEs show activation energy barriers comparable to that of wild-type Zn-Zn DapE, their weaker substrate affinity renders these mixed-metal enzymes less efficient. On the other hand, Zn-Co DapE is found to outperform the naturally occurring Zn-Zn DapE, both in terms of substrate affinity and chemical catalysis. The observed metal promiscuity may have played an important role in the survival of bacteria even in those cellular media where Zn ions are in limited supply. Metal nonspecificity in the catalysis of DapE enzyme allows bacteria to thrive in different cellular media.

Monitoring of Fe (II) ions in living cells using a novel quinoline-derived fluorescent probe

Physiologically, Fe(III) and Fe(II) is the most important redox pairs in a variety of biological and environmental procedures with its capability of transition. The detection of physiological iron, especially Fe(II), has become the recent research focus of investigations on revealing the mechanism of iron-related metabolism. In this work, we exploited a novel quinoline-derived fluorescent probe, YTP, for the detection of Fe(II). It could monitor the level of Fe(II) with a linear range of 0-2.0 equivalent and the detection limit of 0.16 µM. High selectivity from other analytes including Fe(III) and steadiness for over 24 h confirmed the practicability of YTP. YTP was further applied in real buffer systems and in cellular imaging. The probe could achieve the semi-quantitative monitoring of Fe(II) in living cells. This work provided a potential implement for the detection of Fe(II), and raised important information for further researches on the redox pairs of iron, in mechanism and in practice.

Catechol oxidation promoted by bridging phenoxo moieties in a bis(μ-phenoxo)-bridged dicopper(ii) complex

A dinuclear copper(ii) complex [Cu₂(papy)₂(CH₃OH)₂] has been synthesized by reaction of one equiv. of Cu(OAc)₂·2H₂O with one equiv. of the tetradentate tripodal ligand H₂papy [N-(2-hydroxybenzyl)-N-(2-picolyl)glycine] and has been characterized by various spectroscopic techniques and its solid state structure has been confirmed by X-ray crystal structure analysis. The single-crystal structure of the complex reveals that the two copper centers are hexa-coordinated and bridged by two O-atoms of the phenoxo moieties. The variable temperature magnetic susceptibility measurement of the complex reveals weak ferromagnetic interactions among the Cu(ii) ions with a J value of 1.1 cm⁻¹. The catecholase activity of the complex has been investigated spectrophotometrically using 3,5-di-tert-butyl catechol as a model substrate in methanol solvent under aerobic conditions. The Michaelis–Menten kinetic treatment has been applied using different excess substrate concentrations. The parameters obtained from the catecholase activity by the complex are K_M 2.97 × 10⁻⁴ M, V_max 2 × 10⁻⁴ M s⁻¹, and k_cat 7.2 × 10³ h⁻¹. A reaction mechanism has been proposed based on experimental findings and theoretical calculations. The catechol substrate binds to dicopper(ii) centers and subsequently two electrons are transferred to the metal centers from the substrate. The bridging phenoxo moieties participate as a Brønsted base by accepting protons from catechol during the catalytic cycle and thereby facilitating the catechol oxidation process.

A bis(μ-phenoxo)-bridged dicopper(ii) complex capable of oxidizing catechol with the highest efficiency amongst any bis(μ-phenoxo)-bridged dicopper(ii) complexes is reported.

Controlling the Reactivity of Copper(II) Acylperoxide Complexes

The redox state of the metallomonooxygenases is finely tuned by imposing specific coordination environments on the metal center to reduce the activation energy for the generation of active-oxygen species and subsequent substrate oxygenation reactions. In this study, copper(II) complexes supported by a series of linear tetradentate ligands consisting of a rigid 6-, 7-, or 8-membered cyclic diamine with two pyridylmethyl (-CH₂Py) side arms (L6^Pym2, L7^Pym2, and L8^Pym2) are employed to examine the effects of the coordination environment on the reactivity of their acylperoxide adduct complexes. The UV-vis and electron paramagnetic resonance spectroscopic data indicate that the ligand-field splitting between the d_x²-y² and d_z² orbitals of the starting copper(II) complexes increase with an increase of the ring size of the diamine moiety (L6^Pym2 → L7^Pym2 → L8^Pym2). In the reaction of these copper(II) complexes with m-chloroperbenzoic acid (m-CPBA), the L6^Pym2 complex gives a stable m-CPBA adduct complex, whereas the L7^Pym2 and L8^Pym2 complexes are immediately converted to the corresponding m-chlorobenzoic acid (m-CBA) adducts, indicating that the reactivity of the copper(II) acylperoxide complexes largely depends on the coordination environment induced by the supporting ligands. Density functional theory (DFT) calculations on the m-CPBA adduct complexes show that the ligand-field-splitting energy increases with an increase of the ring size of the diamine moiety, as in the case of the starting copper(II) complexes, which enhances the reactivity of the m-CPBA adduct complexes. The reasons for such different reactivities of the m-CPBA adduct complexes are evaluated by using DFT calculations.

Metal Binding Antimicrobial Peptides in Nanoparticle Bio-functionalization: New Heights in Drug Delivery and Therapy

Peptides are considered very important due to the diversity expressed through their amino acid sequence, structure variation, large spectrum, and their essential role in biological systems. Antimicrobial peptides (AMPs) emerged as a potent tool in therapy owing to their antimicrobial properties but also their ability to trespass the membranes, specificity, and low toxicity. They comprise a variety of peptides from which specific amino acid-rich peptides are of interest to the current review due to their features in metal interaction and cell penetration. Histidine-rich peptides such as Histatins belong to the metal binding salivary residing peptides with efficient antibacterial, antifungal, and wound-healing activities. Furthermore, their ability to activate in acidic environment attracted the attention to their potential in therapy. The current review covers the current knowledge about AMPs and critically assess the potential of associating with metal ions both structurally and functionally. This review provides interesting hints for the advantages provided by AMPs and metal ions in biomedicine, making use of their direct properties in brain diseases therapy or in the creation of new bio-functionalized nanoparticles for cancer diagnosis and treatment.

Survival in Hostile Conditions: Pupylation and the Proteasome in Actinobacterial Stress Response Pathways

Bacteria employ a multitude of strategies to cope with the challenges they face in their natural surroundings, be it as pathogens, commensals or free-living species in rapidly changing environments like soil. Mycobacteria and other Actinobacteria acquired proteasomal genes and evolved a post-translational, ubiquitin-like modification pathway called pupylation to support their survival under rapidly changing conditions and under stress. The proteasomal 20S core particle (20S CP) interacts with ring-shaped activators like the hexameric ATPase Mpa that recruits pupylated substrates. The proteasomal subunits, Mpa and pupylation enzymes are encoded in the so-called Pup-proteasome system (PPS) gene locus. Genes in this locus become vital for bacteria to survive during periods of stress. In the successful human pathogen Mycobacterium tuberculosis, the 20S CP is essential for survival in host macrophages. Other members of the PPS and proteasomal interactors are crucial for cellular homeostasis, for example during the DNA damage response, iron and copper regulation, and heat shock. The multiple pathways that the proteasome is involved in during different stress responses suggest that the PPS plays a vital role in bacterial protein quality control and adaptation to diverse challenging environments.

Ni-Catalyzed Borylation of Aryl Sulfoxides

A nickel/N-heterocyclic carbene (NHC) catalytic system has been developed for the borylation of aryl sulfoxides with B2 (neop)2 (neop=neopentyl glycolato). A wide range of aryl sulfoxides with different electronic and steric properties were converted into the corresponding arylboronic esters in good yields. The regioselective borylation of unsymmetric diaryl sulfoxides was also feasible leading to borylation of the sterically less encumbered aryl substituent. Competition experiments demonstrated that an electron-deficient aryl moiety reacts preferentially. The origin of the selectivity in the Ni-catalyzed borylation of electronically biased unsymmetrical diaryl sulfoxide lies in the oxidative addition step of the catalytic cycle, as oxidative addition of methoxyphenyl 4-(trifluoromethyl)phenyl sulfoxide to the Ni(0) complex occurs selectively to give the structurally characterized complex trans-[Ni(ICy)2 (4-CF3 -C6 H4 ){(SO)-4-MeO-C6 H4 }] 4. For complex 5, the isomer trans-[Ni(ICy)2 (C6 H5 )(OSC6 H5 )] 5-I was structurally characterized in which the phenyl sulfinyl ligand is bound via the oxygen atom to nickel. In solution, the complex trans-[Ni(ICy)2 (C6 H5 )(OSC6 H5 )] 5-I is in equilibrium with the S-bonded isomer trans-[Ni(ICy)2 (C6 H5 )(SOC6 H5 )] 5, as shown by NMR spectroscopy. DFT calculations reveal that these isomers are separated by a mere 0.3 kJ/mol (M06/def2-TZVP-level of theory) and connected via a transition state trans-[Ni(ICy)2 (C6 H5 )(η2 -{SO}-C6 H5 )], which lies only 10.8 kcal/mol above 5.

ASAXS measurements on ferritin and apoferritin at the bioSAXS beamline P12 (PETRA III, DESY)

Small-angle X-ray scattering is widely utilized to study biological macromol-ecules in solution. For samples containing specific (e.g. metal) atoms, additional information can be obtained using anomalous scattering. Here, measuring samples at different energies close to the absorption edges of relevant elements provides specific structural details. However, anomalous small-angle X-ray scattering (ASAXS) applications to dilute macromolecular solutions are challenging owing to the overall low anomalous scattering effect. Here, pilot ASAXS experiments from dilute solutions of ferritin and cobalt-loaded apoferritin are reported. These samples were investigated near the resonance X-ray K edges of Fe and Co, respectively, at the EMBL P12 bioSAXS beamline at PETRA III, DESY. Thanks to the high brilliance of the P12 beamline, ASAXS experiments are feasible on dilute protein solutions, allowing one to extract the Fe- or Co-specific anomalous dispersion terms from the ASAXS data. The data were subsequently used to determine the spatial distribution of either iron or cobalt atoms incorporated into the ferritin/apoferritin protein cages.

Resolution of Low-Energy States in Spin-Exchange Transition-Metal Clusters: Case Study of Singlet States in [Fe(III)4S4] Cubanes

Polynuclear transition-metal (PNTM) clusters owe their catalytic activity to numerous energetically low-lying spin states and stable oxidation states. The characterization of their electronic structure represents one of the greatest challenges of modern chemistry. We propose a theoretical framework that enables the resolution of targeted electronic states with ease and apply it to two [Fe(III)₄S₄] cubanes. Through direct access to their many-body wave functions, we identify important correlation mechanisms and their interplay with the geometrical distortions observed in these clusters, which are core properties in understanding their catalytic activity. The simulated magnetic coupling constants predicted by our strategy allow us to make qualitative connections between spin interactions and geometrical distortions, demonstrating its predictive power. Moreover, despite its simplicity, the strategy provides magnetic coupling constants in good agreement with the available experimental ones. The complexes are intrinsically frustrated anti-ferromagnets, and the obtained spin structures together with the geometrical distortions represent two possible ways to release spin frustration (spin-driven Jahn–Teller distortion). Our paradigm provides a simple, yet rigorous, route to uncover the electronic structure of PNTM clusters and may be applied to a wide variety of such clusters.

Effect of structural variation on enzymatic activity in tetranuclear (Cu4) clusters with defective cubane core

The stimulus to the modeling of enzyme functioning sites comes from their potential to give insight into the natural enzyme's mechanistic pathways, ascertain the role of that different metal ion in the active site and construct better catalysts motivated by nature. The presence of metal ion leads to the activation of molecular oxygen in the metalloenzymes. The metalloenzymes such as the catechol oxidase (CO) enzyme that oxidizes the catechol to corresponding quinones which eventually protect damage tissues from plant and pathogen. Thus, the design and characterization of catalysts used as selectively and efficiently oxidation reactions have grown to be unique challenges for modern inorganic chemists. In this work, two novel tetranuclear complexes (1 and 2) have been synthesized in excellent yield. The complexes were characterized using various spectroscopic techniques such as FTIR, UV-Visible and PXRD pattern. The structure of 1 and 2 was elucidated by SC-XRD (single crystal X-ray diffraction) analysis. The magnetic study reveals the presence of the antiferromagnetic nature of 1 and 2. Both 1 and 2 shows a very good catecholase-like activity by oxidizing the catechol to analogous quinone in methanolic solution. Thus, a structure-activity relationship can further help us design other substituted tetranuclear complexes with enhanced catecholase like activity.Communicated by Ramaswamy H. Sarma.

Copper binding and reactivity at the histidine brace motif: insights from mutational analysis of the Pseudomonas fluorescens copper chaperone CopC

The histidine brace (His-brace) is a copper-binding motif that is associated with both oxidative enzymes and proteinaceous copper chaperones. Here, we used biochemical and structural methods to characterize mutants of a His-brace-containing copper chaperone from Pseudomonas fluorescens (PfCopC). A total of 15 amino acid variants in primary and second-sphere residues were produced and characterized in terms of their copper binding and redox properties. PfCopC has a very high affinity for Cu(II) and also binds Cu(I). A high reorganization barrier likely prevents redox cycling and, thus, catalysis. In contrast, mutations in the conserved second-sphere Glu27 enable slow oxidation of ascorbate. The crystal structure of the variant E27A confirmed copper binding at the His-brace. Unexpectedly, Asp83 at the equatorial position was shown to be indispensable for Cu(II) binding in the His-brace of PfCopC. A PfCopC mutant that was designed to mimic the His-brace from lytic polysaccharide monooxygenase-like family X325 did not bind Cu(II), but was still able to bind Cu(I). These results highlight the importance of the proteinaceous environment around the copper His-brace for reactivity and, thus, the difference between enzyme and chaperone.

Vanadium aminophenolates in catechol oxidation: conformity with Finke's common catalyst hypothesis

Six known aminophenolate vanadium complexes V1-V6 were examined in 3,5-di-tert-butylcatechol (1, 3,5-DTBC) oxidation. From the complexes V1-V5 have been previously shown to demonstrate catechol oxidase (catecholase) like behavior, catalytically oxidizing 1 to 3,5-di-tert-butyl-1,2-benzoquinone (2, 3,5-DTBQ). A critical re-evaluation of V1-V5, including V6 not assessed earlier, in the aerobic oxidation of 1 has revealed that several catechol dioxygenase products are obtained in addition to 2, which is produced partly by autoxidation. Mechanistic investigations into the V1-V6 catalyzed oxidation of 1 by EPR, negative mode ESI-MS and 51V NMR, in addition to semi-quantitative product distribution analyses with GC and column chromatography afford compelling evidence in support of the "common catalyst hypothesis" earlier proposed by Finke and co-workers. During the reaction, V1-V6 are partially converted in situ by H2O2 assisted leaching to vanadium catecholate complexes [V(3,5-DTBC)2(3,5-DTBSQ˙)] and [VO(3,5-DTBC)(3,5-DTBSQ˙)], where 3,5-DTBSQ˙ = 3,5-di-tert-butyl-1,2-semiquinone, the latter of which has been implicated as the common true active catalyst in catechol dioxygenation as per the common catalyst hypothesis. The results herein suggest that vanadium aminophenolate complexes are sensitive to H2O2 mediated leaching in the presence of strong σ and π donating ligands such as 1 and 2. Furthermore, based on these results, the use of vanadium aminophenolate complexes as catechol oxidase mimics is not as warranted as previously understood.

Synthesis and Reactivity Studies of a Series of Nickel(II) Arylchalcogenolates

Two series of high-spin nickel complexes, [Tp^Ph,Me]Ni(EAr) (E = O, Se, Te; Ar = C₆H₅) and [Tp^Ph,Me]Ni(SeC₆H₄-4-X) (X = H, Cl, Me, OMe), were prepared by metathetical reaction of the nickel(II) halide precursor with sodium salts of the corresponding chalcogen, NaEAr. X-ray crystallographic characterization and spectroscopic studies have established the geometric and electronic structures of these complexes. The observed spectroscopic and structural characteristics reveal distinct trends in accordance with the variation of the identity of the arylchalcogenolate and para substituent. Reaction of the [Tp^Ph,Me]Ni(EAr) complexes with methyl iodide proceeded readily, producing the corresponding methylarylchalcogen and [Tp^Ph,Me]NiI. A kinetic and computational analysis of the reaction of [Tp^Ph,Me]Ni(SeC₆H₅) with MeI supports that the electrophilic alkylation reactions occur via an associative mechanism via a classical S_N2 transition state.

Evaluation of metal-based antimicrobial compounds for the treatment of bacterial pathogens

Antimicrobial resistance (AMR) is one of the greatest global health challenges of modern times and its prevalence is rising worldwide. AMR within bacteria reduces the efficacy of antibiotics and increases both the morbidity and the mortality associated with bacterial infections. Despite this growing risk, few antibiotics with a novel mode of action are being produced, leading to a lack of antibiotics that can effectively treat bacterial infections with AMR. Metals have a history of antibacterial use but upon the discovery of antibiotics, often became overlooked as antibacterial agents. Meanwhile, metal-based complexes have been used as treatments for other diseases, such as the gold-containing drug auranofin, used to treat rheumatoid arthritis. Metal-based antibacterial compounds have novel modes of action that provide an advantage for the treatment of bacterial infections with resistance to conventional antibiotics. In this review, the antibacterial activity, mode of action, and potential for systemic use of a number of metal-based antibacterial complexes are discussed. The current limitations of these compounds are highlighted to determine if metal-based agents are a potential solution for the treatment of bacterial infections, especially those resistant to conventional antibiotics.

Putting amino acids onto tRNAs: The aminoacyl-tRNA synthetases as catalysts

In this chapter we consider the catalytic approaches used by aminoacyl-tRNA synthetase (AARS) enzymes to synthesize aminoacyl-tRNA from cognate amino acid and tRNA. This ligase reaction proceeds through an activated aminoacyl-adenylate (aa-AMP). Common themes among AARSs include use of induced fit to drive catalysis and transition state stabilization by class-conserved sequence and structure motifs. Active site metal ions contribute to the amino acid activation step, while amino acid transfer to tRNA is generally a substrate-assisted concerted mechanism. A distinction between classes is the rate-limiting step for aminoacylation. We present some examples for each aspect of aminoacylation catalysis, including the experimental approaches developed to address questions of AARS chemistry.

Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress

The ability of pathogens to maintain homeostatic levels of essential biometals is known to be important for survival and virulence in a host, which itself regulates metal availability as part of its response to infection. Given this importance of metal homeostasis, we sought to address how the availability of copper in particular impacts the response of the opportunistic fungal pathogen Candida albicans to treatment with the antifungal drug fluconazole. The present study reports whole transcriptome analysis via time-course RNA-seq of C. albicans cells exposed to fluconazole with and without 10 µM supplemental CuSO₄ added to the growth medium. The results show widespread impacts of small changes in Cu availability on the transcriptional response of C. albicans to fluconazole. Of the 2359 genes that were differentially expressed under conditions of cotreatment, 50% were found to be driven uniquely by exposure to both Cu and fluconazole. The breadth of metabolic processes that were affected by cotreatment illuminates a fundamental intersectionality between Cu metabolism and fungal response to drug stress. More generally, these results show that seemingly minor fluctuations in Cu availability are sufficient to shift cells’ transcriptional response to drug stress. Ultimately, the findings may inform the development of new strategies that capitalize on drug-induced vulnerabilities in metal homeostasis pathways.

Buffered Coordination Modulation as a Means of Controlling Crystal Morphology and Molecular Diffusion in an Anisotropic Metal-Organic Framework

Significant advances have been made in the synthesis of chemically selective environments within metal-organic frameworks, yet materials development and industrial implementation have been hindered by the inability to predictively control crystallite size and shape. One common strategy to control crystal growth is the inclusion of coordination modulators, which are molecular species designed to compete with the linker for metal coordination during synthesis. However, these modulators can simultaneously alter the pH of the reaction solution, an effect that can also significantly influence crystal morphology. Herein, noncoordinating buffers are used to independently control reaction pH during metal-organic framework synthesis, enabling direct interrogation of the role of the coordinating species on crystal growth. We demonstrate the efficacy of this strategy in the synthesis of low-dispersity single-crystals of the framework Co₂(dobdc) (dobdc^4-= 2,5-dioxido-1,4-benzenedicarboxylate) in a pH 7-buffered solution using cobalt(II) acetate as the metal source. Density functional theory calculations reveal that acetate competitively binds to Co during crystallization, and by using a series of cobalt(II) salts with carboxylate anions of varying coordination strength, it is possible to control crystal growth along the c-direction. Finally, we use zero length column chromatography to show that crystal morphology has a direct impact on guest diffusional path length for the industrially important hydrocarbon m-xylene. Together, these results provide molecular-level insight into the use of modulators in governing crystallite morphology and a powerful strategy for the control of molecular diffusion rates within metal-organic frameworks.

Electrophilic Modulation of the Superoxide Anion Radical Scavenging Ability of Copper(II) Complexes with 4-Methyl Imidazole

Three Cu(II) coordination compounds with 4-methyl imidazole were obtained, such as [Cu(C₄H₆N₂)₄(NO₃)₂], [Cu(C₄H₆N₂)₄Br₂], and [Cu(C₄H₆N₂)₄Cl₂]. Crystallographic studies confirmed their structural similarity with Cu(II) in the active site of endogenous copper-zinc superoxide dismutase (CuZn-SOD). The superoxide anion radical (O₂^•-) scavenging activity was evaluated by the non-enzymatic experimental assay and followed the trend [Cu(C₄H₆N₂)₄(NO₃)₂] > [Cu(C₄H₆N₂)₄Br₂] > [Cu(C₄H₆N₂)₄Cl₂]. The density functional theory and the hard and soft acids and bases principle showed the importance of the electron-deficient character of Cu(II) in the chemical reactivity of the coordination compounds; Cu(II) is the softest site in the molecule and it is preferred for the nucleophilic and radical attacks of the soft O₂^•-. A simple rule was obtained: "the electron-deficient character of Cu(II) is the key index for the O₂^•- scavenging activity and is modulated by the electron-releasing counteranion effect on the coordination compound".

Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models

Commonly seen in rare-earth chemistry and materials science, highly charged metal ions play key roles in many chemical processes. Computer simulations have become an important tool for scientific research nowadays. Meaningful simulations require reliable parameters. In the present work, we parametrized 18 M(III) and 6 M(IV) metal ions for four new water models (OPC3, OPC, TIP3P-FB, TIP4P-FB) in conjunction with each of the 12-6 and 12-6-4 nonbonded models. Similar to what was observed previously, issues with the 12-6 model can be fixed by using the 12-6-4 model. Moreover, the four new water models showed comparable performance or considerable improvement over the previous water models (TIP3P, SPC/E, and TIP4P_EW) in the same category (3-point or 4-point water models, respectively). Finally, we reported a study of a metalloprotein system demonstrating the capability of the 12-6-4 model to model metalloproteins. The reported parameters will facilitate accurate simulations of highly charged metal ions in aqueous solution.

Bioactive Tryptophan-Based Copper Complex with Auxiliary β-Carboline Spectacle Potential on Human Breast Cancer Cells: In Vitro and In Vivo Studies

Biocompatible tryptophan-derived copper (1) and zinc (2) complexes with norharmane (β-carboline) were designed, synthesized, characterized, and evaluated for the potential anticancer activity in vitro and in vivo. The in vitro cytotoxicity of both complexes 1 and 2 were assessed against two cancerous cells: (human breast cancer) MCF7 and (liver hepatocellular cancer) HepG2 cells with a non-tumorigenic: (human embryonic kidney) HEK293 cells. The results exhibited a potentially decent selectivity of 1 against MCF7 cells with an IC50 value of 7.8 ± 0.4 μM compared to 2 (less active, IC50 ~ 20 μM). Furthermore, we analyzed the level of glutathione, lipid peroxidation, and visualized ROS generation to get an insight into the mechanistic pathway and witnessed oxidative stress. These in vitro results were ascertained by in vivo experiments, which also supported the free radical-mediated oxidative stress. The comet assay confirmed the oxidative stress that leads to DNA damage. The histopathology of the liver also ascertained the low toxicity of 1.

Modular Design of G-Quadruplex MetalloDNAzymes for Catalytic C-C Bond Formations with Switchable Enantioselectivity

Metal-binding DNA structures with catalytic function are receiving increasing interest. Although a number of metalloDNAzymes have been reported to be highly efficient, the exact coordination/position of their catalytic metal center is often unknown. Here, we present a new approach to rationally develop metalloDNAzymes for Lewis acid-catalyzed reactions such as enantioselective Michael additions. Our strategy relies on the predictable folding patterns of unimolecular DNA G-quadruplexes, combined with the concept of metal-mediated base-pairing. Transition-metal coordination environments were created in G-quadruplex loop regions, accessible by substrates. Therefore, protein-inspired imidazole ligandoside L was covalently incorporated into a series of G-rich DNA strands by solid-phase synthesis. Iterative rounds of DNA sequence design and catalytic assays allowed us to select tailored metalloDNAzymes giving high conversions and excellent enantioselectivities (≥99%). Based on their primary sequence, folding pattern, and metal coordination mode, valuable information on structure-activity relationships could be extracted. Variation of the number and position of ligand L within the sequence allowed us to control the formation of (S) and (R) enantiomeric reaction products, respectively.

Evaluating the anticancer properties and real-time electrochemical extracellular bio-speciation of bis (1,10-phenanthroline) silver (I) acetate monohydrate in the presence of A549 lung cancer cells

According to the American Cancer Society report (2019-2021), the majority (63%) of stage III non-small cell lung cancer (NSCLC) patients are prescribed with chemo and/or radiation therapies, with 5-year relative survival rates of just 19%. Thus, directed drug development, toward personalised cancer treatment, is widely recognised as a necessary strategy in drug discovery research. However, broad generalisations on the modes of action of bioinorganic compounds are not conducive to tailored drug design, hence, fundamental mechanistic research is essential in realising personalised healthcare. In this work, anticancer properties of bis (1,10-phenanthroline) silver (I) acetate monohydrate (Ag-Phen), toward A549 lung cancer cells are presented. Biological assays were carried out to evaluate the effect of Ag-Phen on cell viability, reactive oxygen species generation and mitochondrial membrane potentials. In tandem with the biological assays, electrochemistry was employed to determine the real-time concentrations of intact Ag-Phen and dissociated Ag⁺ in the extracellular medium using platinum microelectrodes, as a function of cellular exposure time. Observations from the assays conducted include, Ag-Phen induced cytotoxicity (IC₅₀ 4.5 μM at 72 h) and 2-fold ROS generation, and a 50% decrease in mitochondrial membrane potentials with respect to equivalent concentrations of Ag⁺ and 1,10-phenanthroline. Bio-speciation studies, conducted electrochemically at platinum microelectrodes, revealed almost 50% of the Ag-Phen had dissociated after 2 h. Significant reductions in concentrations of dissociated Ag⁺ (from 67.7 μM to 6.7 μM), and the Ag-Phen complex (from 50.2 μM to 11.7 μM) between 4 and 24 h from the extracellular medium, indicate cellular uptake of both. This novel method facilitates the real-time identification and quantification of electroactive species, both the intact Ag-Phen and Ag⁺, in the presence of A549 cells.

In situ Generation of Antibiotics using Bioorthogonal "Nanofactories"

Prodrug strategies use chemical modifications to improve the pharmacokinetic properties and therefore therapeutic effects of parent drugs. Traditional prodrug approaches use endogenous enzymes for activation. Bioorthogonal catalysis uses processes that endogenous enzymes cannot access, providing a complementary strategy for prodrug uncaging. Site-selective activation of prodrugs to drugs (uncaging) using synthetic catalysts is a promising strategy for localized drug activation. We discuss here recent studies that incorporate metal catalysts into polymers and nanoparticle scaffolds to provide biocompatible "enzyme-like" catalysts that can penetrate bacterial biofilms and activate prodrug antibiotics in situ, affording a new strategy to treat bacterial biofilm infections with the potential for reduced off-target effects.

Fluorescent iron‑sulfur centers: Photochemistry of the PetA Rieske protein from Aquifex aeolicus

Cytochrome bc₁ complexes are energy-transducing enzymes and key components of respiratory electron chains. They contain Rieske 2Fe2S proteins that absorb very weakly in the visible absorption region compared to the heme cofactors of the cytochromes, but are known to yield photoproducts. Here, the photoreactions of isolated Rieske proteins from the hyperthermophilic bacterium Aquifex aeolicus are studied in two redox states using ultrafast transient fluorescence and absorption spectroscopy. We provide evidence, for the first time in iron‑sulfur proteins, of very weak fluorescence of the excited state, in the oxidized as well as the reduced state. The excited states of the oxidized and reduced forms decay in 1.5 ps and 30 ps, respectively. In both cases they give rise to product states with lifetimes beyond 1 ns, reflecting photo-reduction of oxidized centers as well as photo-oxidation of reduced centers. Potential reaction partners are discussed and studied using site-directed mutagenesis. For the reduced state, a nearby disulfide bridge is suggested as an electron acceptor. The resulting photoproducts in either state may play a role in photoactivation processes.

Optimization of Initial Cation Concentrations for L-Lactic Acid Production from Fructose by Lactobacillus pentosus Cells

In this study, Box-Behnken design was applied to optimize the initial concentrations of 4 cations for L-lactic acid production from fructose by homologous batch fermentation of Lactobacillus pentosus cells. The optimum initial cation concentrations were obtained as 6.542 mM Mg²⁺, 3.765 mM Mn²⁺, 2.397 mM Cu²⁺, and 3.912 mM Fe²⁺, respectively. The highest L-lactic acid yield and productivity were obtained as 0.935 ± 0.005 g/g fructose and 1.363 ± 0.021 g/(L × h), respectively, with a maximum biomass concentration of 7.97 ± 0.17 g/L. The effectiveness of the optimization by Box-Behnken design was confirmed based on the small errors between predicted results and experimental results shown as 0.3%, - 0.2%, and - 1.2%, respectively. The quadratic models with high accuracy and reliability can be applied to mathematically forecasted the fermentation performance. After the optimization, the lactic acid yield and productivity were significantly improved by 3.7% and 21.0%, respectively.

A Quantum Chemistry View on Two Archetypical Paramagnetic Pentacoordinate Nickel(II) Complexes Offers a Fresh Look on Their NMR Spectra

Quantum chemical methods for calculating paramagnetic NMR observables are becoming increasingly accessible and are being included in the inorganic chemistry practice. Here, we test the performance of these methods in the prediction of proton hyperfine shifts of two archetypical high-spin pentacoordinate nickel(II) complexes (NiSAL-MeDPT and NiSAL-HDPT), which, for a variety of reasons, turned out to be perfectly suited to challenge the predictions to the finest level of detail. For NiSAL-MeDPT, new NMR experiments yield an assignment that perfectly matches the calculations. The slightly different hyperfine shifts from the two “halves” of the molecules related by a pseudo-C₂ axis, which are experimentally divided into two well-defined spin systems, are also straightforwardly distinguished by the calculations. In the case of NiSAL-HDPT, for which no X-ray structure is available, the quality of the calculations allowed us to refine its structure using as a starting template the structure of NiSAL-MeDPT.

State-of-the-art quantum chemical methods and paramagnetism-tailored NMR experiments provide a deep insight on the relation between the spectra and the electronic structure for two paramagnetic pentacoordinate nickel(II) complexes.

A new air-stable Si,S-chelating ligand for Ir-catalyzed directed ortho C-H borylation

A new air-stable Si,S-chelating ligand has been developed and used in an iridium-catalyzed ortho C-H borylation reaction with a broad substrate scope. This study provides the first example of using a sulfur-containing ligand in the catalytic C-H borylation process. It provides a rapid, efficient, and economical method for the preparation of organoboron compounds.

Nanozymes for Environmental Pollutant Monitoring and Remediation

Nanozymes are advanced nanomaterials which mimic natural enzymes by exhibiting enzyme-like properties. As nanozymes offer better structural stability over their respective natural enzymes, they are ideal candidates for real-time and/or remote environmental pollutant monitoring and remediation. In this review, we classify nanozymes into four types depending on their enzyme-mimicking behaviour (active metal centre mimic, functional mimic, nanocomposite or 3D structural mimic) and offer mechanistic insights into the nature of their catalytic activity. Following this, we discuss the current environmental translation of nanozymes into a powerful sensing or remediation tool through inventive nano-architectural design of nanozymes and their transduction methodologies. Here, we focus on recent developments in nanozymes for the detection of heavy metal ions, pesticides and other organic pollutants, emphasising optical methods and a few electrochemical techniques. Strategies to remediate persistent organic pollutants such as pesticides, phenols, antibiotics and textile dyes are included. We conclude with a discussion on the practical deployment of these nanozymes in terms of their effectiveness, reusability, real-time in-field application, commercial production and regulatory considerations.

Insights into metalloproteins and metallodrugs from electron paramagnetic resonance spectroscopy

Metal ions play an important role in diverse biological processes, and much of the basic knowledge derived from studying native bioinorganic systems are applied in the synthesis of new molecules with the aim of diagnosing and treating diseases. At first glance, metalloproteins and metallodrugs are very different systems, but metal ion coordination, redox chemistry and substrate binding play essential roles in advancing both of these research fields. In this article, we discuss recent metalloprotein and metallodrug studies where electron paramagnetic resonance spectroscopy served as a major tool to gain a better understanding of metal-based structures and their function.

Recyclable aqueous metal adsorbent: Synthesis and Cu(II) sorption characteristics of ternary nanocomposites of Fe3O4 nanoparticles@graphene-poly-N-phenylglycine nanofibers

Metal pollutant adsorbents are an essential material platform for sustainable environmental remediation, but the adsorbents are typically disposable after sorption, which secondarily contaminates the environment. We report on recyclable Cu(II) adsorbent of deprotonated poly-N-phenylglycine nanofibers (d-PPG NFs)-grafted reduced graphene oxide (rGO) sheets intercalated with Fe₃O₄ nanoparticles (NPs), which are synthesized via wet chemical process. The adsorption performances of ternary Fe₃O₄ NPs@rGO-d-PPG NFs and binary Fe₃O₄ NPs@rGO composites are compared, and the ternary ones exhibit much higher Cu²⁺-adsorption capacity than binary ones under diverse pH conditions due to both high specific surface area and high cationic affinity of d-PPG NFs that follow the Freundlich adsorption model. Density-functional theory calculation results explain why/how the ternary composites show greater Cu²⁺ adsorption capability in higher pH environment. The ternary composites present stable, high Cu²⁺ adsorption capability, irrespective of Co²⁺ concentration in bimetallic Cu and Co aqueous solution. The Fe₃O₄ NPs in the ternary composites allow magnet-assisted collection after adsorption batches, whose collection yield is ∼95 % without adsorption capacity degradation in repeated adsorbent reuses over 10 times. This study provides a general, promising pathway to synthesize reusable sorptive materials for water purification/remediation.

Tetranuclear copper(ii) cubane complexes derived from self-assembled 1,3-dimethyl-5-(o-phenolate-azo)-6-aminouracil: structures, non-covalent interactions and magnetic property

A new doubly opened 4 + 2 Cu₄O₄ cubane cluster exhibits strong antiferromagnetic exchange coupling with J₁ = −110.1 cm⁻¹, and J₂ = −27.1 cm⁻¹.

Facile intramolecular crosslinking of polymers by metallic coordination in concentrated solutions

Single chain nanoparticles are obtained by intramolecular metallic coordination in concentrated solutions at ambient temperature.

Core–shell ZIF-8@polydopamine nanoparticles obtained by mitigating the polydopamine coating induced self-etching of MOFs: prototypical metal ion reservoirs for sticking to and killing bacteria

ZIF-8@PDA nanoparticles can work as metal ion reservoirs that locally release metal ions to kill bacteria after sticking to them.

Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources

Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.

Molecular and heterogeneous water oxidation catalysts: recent progress and joint perspectives

The recent synthetic and mechanistic progress in molecular and heterogeneous water oxidation catalysts highlights the new, overarching strategies for knowledge transfer and unifying design concepts.