Configurations of Nickel-Cyclam Antiviral Complexes and Protein Recognition

Unusual Ni⋯Ni interaction in Ni(ii) complexes as potential inhibitors for the development of new anti-SARS-CoV-2 Omicron drugs

Two nickel(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) of a tetradentate Schiff base ligand (H2L) derived from 2-hydroxy-1-naphthaldehyde with ethylenediamine were synthesized, designed, and characterized via spectroscopic and single crystal XRD analyses. Both nickel(ii) complexes exhibited unusual Ni⋯Ni interactions and were fully characterized via single-crystal X-ray crystallography. Nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) crystallize in monoclinic and triclinic crystal systems with P21/c and P1̄ space groups, respectively, and revealed square planar geometry around each Ni(ii) ion. The structure of both the complexes have established the existence of a new kind of metal system containing nickel(ii)-nickel(ii) interactions with a square planar-like geometry about the nickel(ii) atoms. Both square planar Ni(ii) complexes were often stacked with relatively short Ni⋯Ni distances. The non-bonded Ni-Ni distance (Ni⋯Ni separation) seems to be 3.356 Å and 3.214 Å from the nickel atoms of [Ni(L)]2(1) and [Ni(L)]n(2), respectively. These distances are shorter than the sum of their van der Waals radii (4.80 Å) but longer than the sum of their covalent radii (2.50 Å), indicating that there is a Ni⋯Ni interaction but not a Ni-Ni bond. The discrete molecules are π-stacked and connected via weak intermolecular interactions (C-H⋯O and C-H⋯N). Cyclic voltammetry measurements were obtained for both the complexes, and their pharmacokinetic and chemoinformatics properties were also explored. Detailed structural analysis and non-covalent supramolecular interactions were investigated using single-crystal structure analysis and computational approaches. Both the unique structures show good inhibition performance for the Omicron spike proteins of the SARS CoV-2 virus. To gain insights into potential SARS-CoV-2 Omicron drugs and find inhibitors against the Omicron variants of SARS-CoV-2, we examined the molecular docking of the nickel(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron spike protein (PDB ID: 7WK2 and 7WVO). A strong binding was predicted between Ni(ii) coordination complexes [Ni(L)]2(1) and [Ni(L)]n(2) with the SARS-CoV-2 Omicron variant receptor protein through the negative value of binding affinity. Molecular docking of Nil(ii) complexes [Ni(L)]2(1) and [Ni(L)]n(2) with a DNA duplex (PDB ID: 7D3T) and RNA (PDB ID: 7TDC) binding protein was also studied. Overall, this study suggests that Ni(ii) complexes can be considered as drug candidates against the Omicron variants of SARS-CoV-2.

Naphthalene Diimide-Tetraazacycloalkane Conjugates Are G-Quadruplex-Based HIV-1 Inhibitors with a Dual Mode of Action

Human immunodeficiency virus 1 (HIV-1) therapeutic regimens consist of three or more drugs targeting different steps of the viral life cycle to limit the emergence of viral resistance. In line with the multitargeting strategy, here we conjugated a naphthalene diimide (NDI) moiety with a tetraazacycloalkane to obtain novel naphthalene diimide (NDI)-tetraazacycloalkane conjugates. The NDI inhibits the HIV-1 promoter activity by binding to LTR G-quadruplexes, and the tetraazacycloalkane mimics AMD3100, which blocks HIV entry into cells by interfering with the CXCR4 coreceptor. We synthesized, purified, and tested the metal-free NDI-tetraazacycloalkane conjugate and the two derived metal-organic complexes (MOCs) that incorporate Cu2+ and Zn2+. The NDI-MOCs showed enhanced binding to LTR G4s as assessed by FRET and CD assays in vitro. They also showed enhanced activity in cells where they dose-dependently reduced LTR promoter activity and inhibited viral entry only of the HIV-1 strain that exploited the CXCR4 coreceptor. The time of addition assay confirmed the dual targeting at the different HIV-1 steps. Our results indicate that the NDI-MOC conjugates can simultaneously inhibit viral entry, by targeting the CXCR4 coreceptor, and LTR promoter activity, by stabilizing the LTR G-quadruplexes. The approach of combining multiple targets in a single compound may streamline treatment regimens and improve the overall patient outcomes.

New nickel(ii) Schiff base complexes as potential tools against SARS-CoV-2 Omicron target proteins: an in silico approach

Herein, we report the in silico design and synthesis of two new nickel(ii) coordination complexes, based on Schiff bases derived from the 2-hydroxy-1-naphthaldehyde moiety.

Synthesis of and Metal Complexation with a Chiral Cyclam

Tetraazamacrocycles, like cyclam 1, are well-studied polyamine ligands for metal ions that were first developed to model biological processes. Despite being studied for nearly 60 years, the development of chiral variants of 1 has been limited. We report the synthesis of a chiral variant of 1, the tetraazamacrocycle 2. Outlined herein are the synthesis of 2, a preliminary study of its complexation with metal ions, and the properties of the resulting metal complexes.

The role of coordination compounds in virus research. Different approaches and trends

This article aims to provide an overview of the studies focused on using coordination compounds as antiviral agents against different types of viruses. We present various strategies so far used to this end. This article is divided into two sections. The first collects the series of designed antiviral drugs based on coordination compounds. This approach has been developed for many years, starting from the 70s with the discovery of cis-platin (cis-DDP). It has been mainly focused on studying the synergistic effect of a wide variety of new compounds obtained by combining metal ions with organic antiviral ligands. Then, we collect various strategies analyzing the coordination compounds interacting with viruses using different processes such as wrapping viruses, rapid detection of RNA or DNA virus, or nanocarriers. These recent and novel insights help to study viruses from other points of view, allowing to measure their physical and chemical properties. We also highlight a section in which the issue of viruses from a disinfection viewpoint is addressed, using coordination compounds as a tool able to control the release of antiviral and biocide agents. This is an emerging and promising field but this approach is actually little developed. We finally provide a section with a general conclusion and perspectives.

Transition metal complexes as potential tools against SARS-CoV-2: anin silicoapproach

Screening of selected transition metal-based antiviral agents,in silico, predicted the potential inhibition of RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 which emerged as the potential drug candidate for COVID-19.

Acetate as a model for aspartate-based CXCR4 chemokine receptor binding of cobalt and nickel complexes of cross-bridged tetraazamacrocycles

A number of disease states including WHIM syndrome, HIV infection and cancer have been linked to the chemokine receptor CXCR4. High-affinity CXCR4 antagonist transition metal complexes of configurationally restricted bis-tetraazamacrocyclic ligands have been identified in previous studies. Recently synthesised and structurally characterised Co2+/Co3+ and Ni2+ acetate complexes of mono-macrocycle cross-bridged ligands have been used to mimic their known coordination interaction with the aspartate side chains on binding to CXCR4. Here, X-ray crystal structures for three Co2+/Co3+ acetate complexes and five Ni2+ acetate complexes are presented and demonstrate flexibility in the mode of binding to the acetate ligand concomitantly with the requisite cis-V-configured cross-bridged tetraazamacrocyle. Complexes of the smaller Co3+ metal ion exclusively bind acetate by chelating both oxygens of acetate. Larger Co2+ and Ni2+ metal ions in cross-bridged tetraazamacrocycles show a clear tendency to coordinate acetate in a monodentate fashion with a coordinated water molecule completing the octahedral coordination sphere. However, in unbridged tetraazamacrocycle acetate structures reported in the literature, the coordination preference is to chelate both acetate oxygens. We conclude that the short ethylene cross-bridge restricts the equatorial bulk of the macrocycle, prompting the metal ion to fill the equator with the larger monodentate acetate plus water ligand set. In unbridged ligand examples, the flexible macrocycle expands equatorially and generally only allows chelation of the sterically smaller acetate alone. These results provide insight for generation of optimised bis-macrocyclic CXCR4 antagonists utilising cobalt and nickel ions.

Water oxidation by Ni(1,4,8,11-tetraazacyclotetradecane)2+ in the presence of carbonate: new findings and an alternative mechanism

The role of nanosized particles or Ni ions on the surface of the electrode under water-oxidation conditions in the presence of Ni(1,4,8,11-tetraazacyclotetradecane)²⁺ was investigated.

Nickel Complexes of C-Substituted Cyclams and Their Activity for CO2 and H+ Reduction

Several nickel(II) complexes of cyclams bearing aryl groups on the carbon backbone were prepared and evaluated for their propensity to catalyze the electrochemical reduction of CO₂ to CO and/or H⁺ to H₂, representing the first catalytic analysis to be performed on an aryl-cyclam metal complex. Cyclic voltammetry (CV) revealed the attenuation of catalytic activity when the aryl group bears the strong electron-withdrawing trifluoromethyl substituent, whereas the phenyl, p-tolyl, and aryl-free derivatives displayed a range of catalytic activities. The gaseous-product distribution for the active complexes was determined by means of controlled-potential electrolysis (CPE) and revealed that the phenyl derivative is the most active as well as the most selective for CO₂ reduction over proton reduction. Stark differences in the activity of the complexes studied are rationalized through comparison of their X-ray structures, absorption spectra, and CPE profiles. Further CV studies on the phenyl derivative were undertaken to provide a kinetic insight.

A direct method for the N-tetraalkylation of azamacrocycles

An efficient protocol for the direct synthesis of N-tetraalkylated derivatives of the azamacrocycles cyclam and cyclen has been developed, using a partially miscible aqueous–organic solvent system with propargyl bromide, benzyl bromide, and related halides. The method works most effectively when the reaction mixture is shaken, not stirred. A crystal structure of the N-tetrapropargyl cyclam derivative 1,4,8,11-tetra(prop-2-yn-1-yl)-1,4,8,11-tetraazacyclotetradecane diperchlorate is reported.

New AMD3100 derivatives for CXCR4 chemokine receptor targeted molecular imaging studies: synthesis, anti-HIV-1 evaluation and binding affinities

CXCR4 is a target of growing interest for the development of new therapeutic drugs and imaging agents as its role in multiple disease states has been demonstrated. AMD3100, a CXCR4 chemokine receptor antagonist that is in current clinical use as a haematopoietic stem cell mobilising drug, has been widely studied for its anti-HIV properties, potential to inhibit metastatic spread of certain cancers and, more recently, its ability to chelate radiometals for nuclear imaging. In this study, AMD3100 is functionalised on the phenyl moiety to investigate the influence of the structural modification on the anti-HIV-1 properties and receptor affinity in competition with anti-CXCR4 monoclonal antibodies and the natural ligand for CXCR4, CXCL12. The effect of complexation of nickel(II) in the cyclam cavities has been investigated. Two amino derivatives were obtained and are suitable intermediates for conjugation reactions to obtain CXCR4 molecular imaging agents. A fluorescent probe (BODIPY) and a precursor for (18)F (positron emitting isotope) radiolabelling were conjugated to validate this route to new CXCR4 imaging agents.

Diaqua[(1R,2S,4R,8R,9S,11R)-2,9-dimethyl-1,4,8,11-tetraazacyclotetradecane]nickel(II) dichloride dihydrate

The crystal structure of the title complex, [Ni(C₁₂H₂₈N₄)(H₂O)₂]Cl₂·2H₂O, displays O—H⋯Cl and O—H⋯O hydrogen bonding. The tetra­aza­cyclo­tetra­decane ligand inter­acts with the Ni^II atom in the cis V configuration and the final two ligand binding sites are occupied by water.

New hexadentate macrocyclic ligand and their copper(II) and nickel(II) complexes: Spectral, magnetic, electrochemical, thermal, molecular modeling and antimicrobial studies

Ni(II) and Cu(II) complexes were synthesized with a hexadentate macrocyclic ligand [3,4,8,9tetraoxo-2,5,7,10tetraaza-1,6dithio-(3,4,8,9) dipyridinedodecane(L)] and characterized by elemental analysis, molar conductance measurements, mass, NMR, IR, electronic, EPR spectral, thermal and molecular modeling studies. All the complexes are 1:2 electrolytes in nature and may be formulated as [M(L)]X(2) [where, M=Ni(II) and Cu(II) and X=Cl(-), NO(3)(-), ½SO(4)(2-), CH(3)COO(-)]. On the basis of IR, electronic and EPR spectral studies an octahedral geometry has been assigned for Ni(II) complexes and tetragonal geometry for Cu(II) complexes. The antimicrobial activities and LD(50) values of the ligand and its complexes, as growth inhibiting agents, have been screened in vitro against two different species of bacteria and plant pathogenic fungi.

A molecular clip throws new light on the complexes formed by a family of cyclam-cored dendrimers with Zn(II) ions. Efficient energy transfer in the heteroleptic complexes

Complexation of Zn(II) ions by cyclam cored dendrimers appended with four (G0), eight (G1) and 16 naphthyl chromophores (G2) at the periphery have been investigated in CH₃CN-CH₂Cl₂ 1 : 1 (v/v) solution by absorption and emission, ESI-mass and ¹H NMR spectroscopy. The results obtained can be interpreted by the formation of complexes of 2 : 1 dendrimer to metal stoichiometry, at low metal ion concentration, and 1 : 1 complexes upon further addition of Zn(II) ions, for all the dendrimer generations. Upon addition of a molecular clip C²⁻ consisting of two anthracene sidewalls bridged by a benzene group with two sulfate substituents in the para positions, heteroleptic complexes of general formula [GnZnC] are formed. Interestingly, in these complexes, a very efficient quenching (practically 100%) of the dendrimer naphthyl luminescence and sensitization (ca. 90%) of the clip anthracene emission take place. The complex [G2ZnC] exhibits a very high molar absorption coefficient in the UV spectral region owing to the 16 naphthyl chromophores of the dendrimer and the two anthracene units of the clip (ε = 1.7 × 10⁵ M⁻¹ cm⁻¹ at 263 nm). Furthermore, the excitation energy absorbed by the naphthyl chromophores is efficiently funneled to the two anthracene units of the clip, which emits in the blue spectral region.

Steady-state and time-resolved studies of the photocleavage of lysozyme by Co(III) complexes

Steady-state and time-resolved studies of site-selective photocleavage of lysozyme by cobalt(III) complexes [Co(NH(3))(5)Br](2+) and ([Co(NH(3))(4)CO(3)](+) are reported. Photocleavage resulted in two fragments of molecular masses approximately 10.5 kDa and approximately 3.5 kDa, and the yield increased (8-33%) with irradiation time (0.16-0.8 h) as well as with the metal complex concentration (0.1-5 mM). The reaction proceeded to a significant extent even when nearly stoichiometric amounts of the reagents were used. Photocleavage was effective at wavelengths ranging from 310 to 390 nm, and cleavage was inhibited by the addition of selected metal ions such as Gd(III) at moderate concentrations (2 mM). Gd(III) is known to bind at Asp52/Glu35 residues on lysozyme, and these residues are located at the enzyme active site. Current and previous studies suggest that Co(III) metal complexes bind at this site on lysozyme. Consistent with this hypothesis, [Co(NH(3))(4)CO(3)](+) (8 mM) inhibited lysozyme activity by 67%. Laser flash photolysis studies show that excitation of the metal complexes [Co(NH(3))(5)Br](2+) and ([Co(NH(3))(4)CO(3)](+) (308 nm, 20 ns pulse width) resulted in the corresponding ligand-derived radical intermediates. For example, photoexcitation of an aqueous solution of [Co(NH(3))(5)Br](2+) at 308 nm resulted in the formation of Br(2)(-*). When the excitation was carried out in the presence of lysozyme, Br(2)(-*) was quenched with a bimolecular rate constant of 1.4 x 10(9) M(-1) s(-1). Quenching resulted in protein-derived radicals (Trp(+*) and Tyr(+*)), as identified by their characteristic known transient absorption bands. Steady-state studies correlated with the time-resolved data, and taken together, these illustrated the reactivities of Co(III) metal complexes to direct protein photocleavage with high selectivity.

Discovery of novel HIV entry inhibitors for the CXCR4 receptor by prospective virtual screening

The process of HIV entry begins with the binding of the viral envelope glycoprotein gp120 to both the CD4 receptor and one of CXCR4 or CCR5 chemokine coreceptors. There is currently considerable interest in developing novel ligands which can attach to these coreceptors and hence block virus-cell fusion. This article compares the application of structure-based (docking) and ligand-based (QSAR analyses, pharmacophore modeling, and shape matching) virtual screening tools to find new potential HIV entry inhibitors for the CXCR4 receptor. The comparison is based on retrospective virtual screening of a library containing different known CXCR4 inhibitors from the literature, a smaller set of active CXCR4 inhibitors selected from a large combinatorial virtual library and synthesized by us, and some druglike presumed inactive molecules as the reference set. The enrichment factors and diversity of the retrieved molecular scaffolds in the virtual hit lists was determined. Once the different virtual screening approaches had been validated and the best parameters had been selected, prospective virtual screening of our virtual library was applied to identify new anti-HIV compounds using the same protocol as in the retrospective virtual screening analysis. The compounds selected using these computational tools were subsequently synthesized and assayed and showed activity values ranging from 4 to 0.022 microg/mL.

Targeting proteins with metal complexes

Unique properties of metal complexes, such as structural diversity, adjustable ligand exchange kinetics, fine-tuned redox activities, and distinct spectroscopic signatures, make them exciting scaffolds not only for binding to nucleic acids but increasingly also to proteins as non-traditional targets. This feature article discusses recent trends in this field. These include the use of chemically inert metal complexes as structural scaffolds for the design of enzyme inhibitors, new strategies for inducing selective coordination chemistry at the protein binding site, recent advances in the development of catalytic enzyme inhibitors, and the design of metal complexes that can inject electrons or holes into redox enzymes. A common theme in many of the discussed examples is that binding selectivity is at least in part achieved through weak interactions between the ligand sphere and the protein binding site. These examples hint to an exciting future in which "organic-like" molecular recognition principles are combined with properties that are unique to metals and thus promise to yield compounds with novel and unprecedented properties.

Metals in membranes

In this critical review we discuss recent advances in understanding the modes of interaction of metal ions with membrane proteins, including channels, pumps, transporters, ATP-binding cassette proteins, G-protein coupled receptors, kinases and respiratory enzymes. Such knowledge provides a basis for elucidating the mechanism of action of some classes of metallodrugs, and a stimulus for the further exploration of the coordination chemistry of metal ions in membranes. Such research offers promise for the discovery of new drugs with unusual modes of action. The article will be of interest to bioinorganic chemists, chemical biologists, biochemists, pharmacologists and medicinal chemists. (247 references).