Erratum: Further correction: Expanding medicinal chemistry into 3D space: metallofragments as 3D scaffolds for fragment-based drug discovery.

[This corrects the article DOI: 10.1039/C9SC05586J.].

Spatial characterization of redox processes and speciation of Ru(III) anticancer complexes by 19F magnetic resonance imaging.

The application of CF3-labeled Ru(III) anticancer complexes to magnetic resonance (MR) imaging of tumour tissues is demonstrated. By combining anatomical chemical-shift selective (CHESS) imaging with 19F chemical-shift imaging (CSI) MR methods, we show that oxidation states and ligand-exchange processes of the complexes can be spatially encoded. Measurements on different tissue models, including a human breast adenocarcinoma tumour, validate the application of these complexes as MR theranostics for the sensing and targeting of hypoxia.

Resolving a Half-Century-Long Controversy between (Magneto)optical and EPR Spectra of Single-Electron-Reduced [PcFe]-, [PcFeL]-, and [PcFeX]2- Complexes: Story of a Double Flip.

The reduction of iron(II) phthalocyanine (Pc(2-)FeII) or its bisaxially coordinated complexes results in the formation of the purple/red [PcFe]-, [PcFeL]-, and [PcFeX]2- (L is neutral and X is anionic ligand) species. The X-ray structure of the [K(DME)4][PcFe] complex exhibits a square-planar [PcFe]- anion. 1H NMR spectra of the reduced species have one or two phthalocyanine broad peaks between 15 and 17 ppm. Solution magnetic moments are consistent with the presence of a single unpaired electron. A solid-state Mössbauer spectrum of [K(DME)4][PcFe] is consistent with an early report [Taube, R. Pure Appl. Chem.1974, 38, 427-438]. The solid-state EPR spectrum of the [PcFe]- anion is close to that recorded by Konarev et al. [ Dalton Trans.2012, 41, 13841-13847]. Solution EPR spectra of reduced species have axial symmetry (g⊥ ∼ 2.08-2.17 and g|| ∼ 1.95-1.96) and correlate well with spectra reported by Lever and Wilshire in 1978 [ Inorg. Chem.1978, 17, 1145-1151]. The UV-vis spectra of pentacoordinated [PcFeL]- and [PcFeX]2- anions consist of the characteristic bands around 810, 690, and 515 nm. These bands correlate well with the set of MCD pseudo A-terms and resemble transitions in the [Pc(3-)M]- and [Pc(3-)ML]- compounds. The UV-vis and MCD spectra of [PcFeL]- and [PcFeX]2- complexes are in stark contrast to the crystallographically characterized reference [Pc(2-)CoI]- anion, which is EPR silent, has a regular diamagnetic 1H NMR spectrum, and has an intense Q-band at 699 nm, which correlates well with the strong MCD A-term. The DFT and TDDFT calculations are suggestive of the iron(II) center in a (dxy)2(dxz,yz)3(dz2)1 (s = 1) electronic configuration that is antiferromagnetically coupled with the one-electron-reduced Pc(3-) ligand (i.e., [Pc(3-)FeII]-, [Pc(3-)FeIIL]-, and [Pc(3-)FeIIX]2-). The calculated EPR, Mössbauer, and UV-vis spectra of [PcFe]-, [PcFeL]-, and [PcFeX]2- complexes are in excellent agreement with the experimental data, thus resolving the controversy between axial s = 1/2 like EPR and Pc(3-)-like UV-vis spectra of these compounds.

Correction: Expanding medicinal chemistry into 3D space: metallofragments as 3D scaffolds for fragment-based drug discovery.

[This corrects the article DOI: 10.1039/C9SC05586J.].

Correction: 19F-Tagged metal binding pharmacophores for NMR screening of metalloenzymes.

Correction for '19F-Tagged metal binding pharmacophores for NMR screening of metalloenzymes' by Kathleen E. Prosser et al., Chem. Commun., 2021, 57, 4934-4937, DOI: 10.1039/D1CC01231B.

Evaluating Metal-Ligand Interactions of Metal-Binding Isosteres Using Model Complexes.

Bioisosteres are a useful approach to address pharmacokinetic liabilities and improve drug-like properties. Specific to developing metalloenzyme inhibitors, metal-binding pharmacophores (MBPs) have been combined with bioisosteres, to produce metal-binding isosteres (MBIs) as alternative scaffolds for use in fragment-based drug discovery (FBDD). Picolinic acid MBIs have been reported and evaluated for their metal-binding ability, pharmacokinetic properties, and enzyme inhibitory activity. However, their structural, electronic, and spectroscopic properties with metal ions other than Zn(II) have not been reported, which might reveal similarities and differences between MBIs and the parent MBPs. To this end, [M(TPA)(MBI)]+ (M = Ni(II) and Co(II), TPA = tris(2-pyridylmethyl)amine) is presented as a bioinorganic model system for investigating picolinic acid, four heterocyclic MBIs, and 2,2'-bipyridine. These complexes were characterized by X-ray crystallography as well as NMR, IR, and UV-vis spectroscopies, and their magnetic moments were accessed. In addition, [(TpPh,Me)Co(MBI)] (TpPh,Me = hydrotris(3,5-phenylmethylpyrazolyl)borate) was used as a second model compound, and the limitations and attributes of the two model systems are discussed. These results demonstrate that bioinorganic model complexes are versatile tools for metalloenzyme inhibitor design and can provide insights into the broader use of MBIs.

19F-Tagged metal binding pharmacophores for NMR screening of metalloenzymes.

This study demonstrates the screening of a collection of twelve 19F-tagged metal-binding pharmacophores (MBPs) against the Zn(ii)-dependent metalloenzyme human carbonic anhydrase II (hCAII) by 19F NMR. The isomorphous replacement of Zn(ii) by Co(ii) in hCAII produces enhanced sensitivity and reveals the potential of 19F NMR-based techniques for metalloenzyme ligand discovery.

Copper(II) Pyridyl Aminophenolates: Hypoxia-Selective, Nucleus-Targeting Cytotoxins, and Magnetic Resonance Probes.

Targeting the low-oxygen (hypoxic) environments found in many tumours by using redox-active metal complexes is a strategy that can enhance efficacy and reduce the side effects of chemotherapies. We have developed a series of CuII complexes with tridentate pyridine aminophenolate-based ligands for preferential activation in the reduction window provided by hypoxic tissues. Furthermore, ligand functionalization with a pendant CF3 group provides a 19 F spectroscopic handle for magnetic-resonance studies of redox processes at the metal centre and behaviour in cellular environments. The phenol group in the ligand backbone was substituted at the para position with H, Cl, and NO2 to modulate the reduction potential of the CuII centre, giving a range of values below the window expected for hypoxic tissues. The NO2 -substituted complex, which has the highest reduction potential, showed enhanced cytotoxic selectivity towards HeLa cells grown under hypoxic conditions. Cell death occurs by apoptosis, as determined by analysis of the cell morphology. A combination of 19 F NMR and ICP-OES indicates localization of the NO2 complex in HeLa cell nuclei and increased cellular accumulation under hypoxia. This correlates with DNA nuclease activity being the likely origin of cytotoxic activity, as demonstrated by cleavage of DNA plasmids in the presence of the CuII nitro complex and a reducing agent. Selective detection of the paramagnetic CuII complexes and their diamagnetic ligands by 19 F MRI suggests hypoxia-targeting theranostic applications by redox activation.

Evaluation of 3-Dimensionality in Approved and Experimental Drug Space.

The 3-dimensional (3D) structure of therapeutics and other bioactive molecules is an important factor in determining the strength and selectivity of their protein-ligand interactions. Previous efforts have considered the strain introduced and tolerated through conformational changes induced upon protein binding. Herein, we present an analysis of 3-dimentionality for energy-minimized structures from the DrugBank and ligands bound to proteins identified in the Protein Data Bank (PDB). This analysis reveals that the majority of molecules found in both the DrugBank and the PDB tend toward linearity and planarity, with few molecules having highly 3D conformations. Decidedly 3D geometries have been historically difficult to achieve, likely due to the synthetic challenge of making 3D organic molecules, and other considerations, such as adherence to the 'rule-of-five'. This has resulted in the dominance of planar and/or linear topologies of the molecules described here. Strategies to address the generally flat nature of these data sets are explored, including the use of 3D organic fragments and inorganic scaffolds as a means of accessing privileged 3D space. This work highlights the potential utility of libraries with greater 3D topological diversity so that the importance of molecular shape to biological behavior can be more fully understood in drug discovery campaigns.

Room temperature aqueous synthesis of UiO-66 derivatives via postsynthetic exchange.

Herein, we report the room temperature aqueous synthesis of the Zr(iv)-based metal-organic framework UiO-66 and a series of functionalized derivatives through postsynthetic exchange from a perfluorinated UiO-66-F4 precursor. All synthesized MOFs in this study were thoroughly characterized to verify formation of the desired MOF, porosity, crystallinity, and exchanged ligand content. This report represents a green, aqueous, room temperature synthesis of a highly valued series of Zr(iv)-based MOFs.

A catalytic antioxidant for limiting amyloid-beta peptide aggregation and reactive oxygen species generation.

Alzheimer's disease (AD) is a multifaceted disease that is characterized by increased oxidative stress, metal-ion dysregulation, and the formation of intracellular neurofibrillary tangles and extracellular amyloid-ß (Aß) aggregates. In this work we report the large affinity binding of the iron(iii) 2,17-bis-sulfonato-5,10,15-tris(pentafluorophenyl)corrole complex FeL1 to the Aß peptide (K d ∼ 10-7) and the ability of the bound FeL1 to act as a catalytic antioxidant in both the presence and absence of Cu(ii) ions. Specific findings are that: (a) an Aß histidine residue binds axially to FeL1; (b) that the resulting adduct is an efficient catalase; (c) this interaction restricts the formation of high molecular weight peptide aggregates. UV-Vis and electron paramagnetic resonance (EPR) studies show that although the binding of FeL1 does not influence the Aß-Cu(ii) interaction (K d ∼ 10-10), bound FeL1 still acts as an antioxidant thereby significantly limiting reactive oxygen species (ROS) generation from Aß-Cu. Overall, FeL1 is shown to bind to the Aß peptide, and modulate peptide aggregation. In addition, FeL1 forms a ternary species with Aß-Cu(ii) and impedes ROS generation, thus showing the promise of discrete metal complexes to limit the toxicity pathways of the Aß peptide.

Expanding medicinal chemistry into 3D space: metallofragments as 3D scaffolds for fragment-based drug discovery.

Fragment-based drug discovery (FBDD) is a powerful strategy for the identification of new bioactive molecules. FBDD relies on fragment libraries, generally of modest size, but of high chemical diversity. Although good chemical diversity in FBDD libraries has been achieved in many respects, achieving shape diversity - particularly fragments with three-dimensional (3D) structures - has remained challenging. A recent analysis revealed that >75% of all conventional, organic fragments are predominantly 1D or 2D in shape. However, 3D fragments are desired because molecular shape is one of the most important factors in molecular recognition by a biomolecule. To address this challenge, the use of inert metal complexes, so-called 'metallofragments' (mFs), to construct a 3D fragment library is introduced. A modest library of 71 compounds has been prepared with rich shape diversity as gauged by normalized principle moment of inertia (PMI) analysis. PMI analysis shows that these metallofragments occupy an area of fragment space that is unique and highly underrepresented when compared to conventional organic fragment libraries that are comprised of orders of magnitude more molecules. The potential value of this metallofragment library is demonstrated by screening against several different types of proteins, including an antiviral, an antibacterial, and an anticancer target. The suitability of the metallofragments for future hit-to-lead development was validated through the determination of IC50 and thermal shift values for select fragments against several proteins. These findings demonstrate the utility of metallofragment libraries as a means of accessing underutilized 3D fragment space for FBDD against a variety of protein targets.

Activation by Oxidation: Ferrocene-Functionalized Ru(II)-Arene Complexes with Anticancer, Antibacterial, and Antioxidant Properties.

Organometallic Ru(II)-cymene complexes linked to ferrocene (Fc) via nitrogen heterocycles have been synthesized and studied as cytotoxic agents. These compounds are analogues of Ru(II)-arene piano-stool anticancer complexes such as RAPTA-C. The Ru center was coordinated by pyridine, imidazole, and piperidine with 0-, 1-, or 2-carbon bridges to Fc to give six bimetallic, dinuclear compounds, and the properties of these complexes were compared with their non-Fc-functionalized parent compounds. Crystal structures for five of the compounds, their Ru-cymene parent compounds, and an unusual trinuclear compound were determined. Cyclic voltammetry was used to determine the formal MIII/II potentials of each metal center of the Ru-cymene-Fc complexes, with distinct one-electron waves observed in each case. The Fc-functionalized complexes were found to exhibit good cytotoxicity against HT29 human colon adenocarcinoma cells, whereas the parent compounds were inactive. Similarly, antibacterial activity from the Ru-cymene-Fc compounds was observed against Bacillus subtilis, but not from the unfunctionalized complexes. In both cases, the IC50 values correlated quantitatively with the Fc+/0 reduction potentials. This is consistent with more facile oxidation to give ferrocenium, and subsequent generation of toxic reactive oxygen species, leading to greater cytotoxicity. The antioxidant properties of the complexes were quantified by a 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay. EC50 values indicate that linking of the Ru and Fc centers promotes antioxidant activity.

Transition Metal Ions Promote the Bioavailability of Hydrophobic Therapeutics: Cu and Zn Interactions with RNA Polymerase†I Inhibitor CX5461.

Low aqueous solubility is a major barrier to the clinical application of otherwise promising drug candidates. We demonstrate that this issue can be resolved in medicinal molecules containing potential ligating groups, through the addition of labile transition-metal ions. Incubation of the chemotherapeutic CX5461 with Cu2+ or Zn2+ enables solubilization at neutral pH but does not affect intrinsic cytotoxicity. Spectroscopic and computational studies demonstrate that this arises from coordination to the pyrazine functionality of CX5461 and may involve bidentate coordination at physiological pH.

Optimal electrostatic interactions between substrate and protein are essential for radical chemistry in ornithine 4,5-aminomutase.

Ornithine 4,5-aminomutase (OAM) from Clostridium sticklandii is an adenosylcobalamin (AdoCbl) and pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes a 1,2-amino shift, interconverting d-ornithine and 2S, 4R-diaminopentanoate. The reaction occurs via a radical-based mechanism whereby a PLP-bound substrate radical undergoes intramolecular isomerization via an azacyclopropylcarbinyl radical intermediate. Herein, we investigated the catalytic role of active site residues that form non-covalent interactions with PLP and/or substrate, d-ornithine. Kinetic analyses revealed that residues that form salt bridges to the α-carboxylate (R297) or the α-amine (E81) of d-ornithine are most critical for OAM activity as conservative substitutions of these residues results in a 300-600-fold reduction in catalytic turnover and a more pronounced 1000- to 14,000-fold decrease in catalytic efficiency. In contrast, mutating residues that solely interact with the PLP cofactor led to more modest decreases (10-60-fold) in kcat and kcat/Km. All but one variant (S162A) elicited an increase in the kinetic isotope effect on kcat and kcat/Km with d,l-ornithine-3,3,4,4,5,5-d6 as the substrate, which indicates that hydrogen atom abstraction is more rate determining. Electron paramagnetic resonance spectra of the variants reveal that while the substitutions decrease the extent of CoC bond homolysis, they do not affect the structural integrity of the active site. Our experimental results, discussed in context with published computational work, suggests that the protonation state of the PLP cofactor has less of a role in radical-mediated chemistry compared to electrostatic interactions between the substrate and protein.

Lowering water oxidation overpotentials using the ionisable imidazole of copper(2-(2'-pyridyl)imidazole).

Rapid and low overpotential oxidation of water to dioxygen remains a key hurdle for storage of solar energy. Here, we address this issue by demonstrating that deprotonation of 2-(2'-pyridyl)-imidazole (pimH)-ligated copper complexes promotes water oxidation at low overpotential and low catalyst loading. This improves upon other work on homogeneous copper-based water oxidation catalysts, which are highly active, but limited by high overpotentials. EPR and UV-vis spectroscopic evaluation of catalyst speciation shows that at pH ≥ 12 coordinated pimH is deprotonated and a bis(hydroxide) Cu2+ active catalyst forms. Rapid electrochemical water oxidation (35 s-1, 0.85 V onset potential) was observed with 150 µM catalyst. These results demonstrate that catalytic water oxidation potentials can be shifted by hundreds of mV in homogeneous metal catalysts bearing an ionisable imidazole ligand.

Anticancer copper pyridine benzimidazole complexes: ROS generation, biomolecule interactions, and cytotoxicity.

The Cu(II) complex CuCl2(pbzH), pbzH=2-(2-pyridyl)benzimidazole, and derivatives modified at the non-coordinated nitrogen of the benzimidazole fragment, have been studied as anticancer agents. These compounds show promising cytotoxicity against A549 adenocarcinomic alveolar basal epithelial cells with IC50 values in the range of 5-10µM. Importantly, this activity is higher than either CuCl2·2H2O or the individual ligands, demonstrating that ligand coordination to the Cu(II) centres of the complexes is required for full activity. Electron paramagnetic resonance (EPR) and UV-Vis spectroscopies were used to characterize the solution behaviour of the complexes. These studies demonstrate: (i) two types of solvated species in buffer, (ii) both coordinate and non-coordinate interactions with albumin, and (iii) weak interactions with DNA. Further DNA studies using agarose gel electrophoresis demonstrate strand cleavage by the complexes in the presence of ascorbate, which is mediated by reactive oxygen species (ROS). Through a fluorescence-based in vitro assay, intracellular ROS generation in the A549 cell line was observed; indicating that damage by ROS is responsible for the observed activity of the complexes.

Combining a Ru(ii)-arene complex with a NO-releasing nitrate-ester ligand generates cytotoxic activity.

A Ru(ii) arene complex with a NO-releasing 4-nitrooxymethyl-pyridine ligand shows increased cytotoxicity against the non-small cell lung cancer cell line A549 as compared to either the free ligand or the unfunctionalized complex. EPR spin-trapping studies show that NO release is selective, being limited in phosphate buffered saline or human serum, but promoted by glutathione.

CF3 Derivatives of the Anticancer Ru(III) Complexes KP1019, NKP-1339, and Their Imidazole and Pyridine Analogues Show Enhanced Lipophilicity, Albumin Interactions, and Cytotoxicity.

The Ru(III) complexes indazolium [trans-RuCl4(1H-indazole)2] (KP1019) and sodium [trans-RuCl4(1H-indazole)2] (NKP-1339) are leading candidates for the next generation of metal-based chemotherapeutics. Trifluoromethyl derivatives of these compounds and their imidazole and pyridine analogues were synthesized to probe the effect of ligand lipophilicity on the pharmacological properties of these types of complexes. Addition of CF3 groups also provided a spectroscopic handle for (19)F NMR studies of ligand exchange processes and protein interactions. The lipophilicities of the CF3-functionalized compounds and their unsubstituted parent complexes were quantified by the shake-flask method to give the distribution coefficient D at pH 7.4 (log D7.4). The solution behavior of the CF3-functionalized complexes was characterized in phosphate-buffered saline (PBS) using (19)F NMR, electron paramagnetic resonance (EPR), and UV-vis spectroscopies. These techniques, along with fluorescence competition experiments, were also used to characterize interactions with human serum albumin (HSA). From these studies it was determined that increased lipophilicity correlates with reduced solubility in PBS but enhancement of noncoordinate interactions with hydrophobic domains of HSA. These protein interactions improve the solubility of the complexes and inhibit the formation of oligomeric species. EPR measurements also demonstrated the formation of HSA-coordinated species with longer incubation. (19)F NMR spectra show that the trifluoromethyl complexes release axial ligands in PBS and in the presence of HSA. In vitro testing showed that the most lipophilic complexes had the greatest cytotoxic activity. Addition of CF3 groups enhances the activity of the indazole complex against A549 nonsmall cell lung carcinoma cells. Furthermore, in the case of the pyridine complexes, the parent compound was inactive against the HT-29 human colon carcinoma cell line but showed strong cytotoxicity with CF3 functionalization. Overall, these studies demonstrate that lipophilicity may be a determining factor in the anticancer activity and pharmacological behavior of these types of Ru(III) complexes.

Electronic Structure Description of a Doubly Oxidized Bimetallic Cobalt Complex with Proradical Ligands.

The geometric and electronic structure of a doubly oxidized bimetallic Co complex containing two redox-active salen moieties connected via a 1,2-phenylene linker was investigated and compared to an oxidized monomeric analogue. Both complexes, namely, CoL(1) and Co2L(2), are oxidized to the mono- and dications, respectively, with AgSbF6 and characterized by X-ray crystallography for the monomer and by vis-NIR (NIR = near-infrared) spectroscopy, electron paramagnetic resonance (EPR) spectroscopy, superconducting quantum interference device (SQUID) magnetometry, and density functional theory (DFT) calculations for both the monomer and dimer. Both complexes exhibit a water molecule coordinated in the apical position upon oxidation. [CoL(1)-H2O](+) displays a broad NIR band at 8500 cm(-1) (8400 M(-1) cm(-1)), which is consistent with recent reports on oxidized Co salen complexes (Kochem, A. et al., Inorg. Chem., 2012, 51, 10557-10571 and Kurahashi, T. et al., Inorg. Chem., 2013, 52, 3908-3919). DFT calculations predict a triplet ground state with significant ligand and metal contributions to the singularly occupied molecular orbitals. The majority (∼75%) of the total spin density is localized on the metal, highlighting both high-spin Co(III) and Co(II)L(•) character in the electronic ground state. Further oxidation of CoL(1) to the dication affords a low-spin Co(III) phenoxyl radical species. The NIR features for [Co2L(2)-2H2O](2+) at 8600 cm(-1) (17 800 M(-1) cm(-1)) are doubly intense in comparison to [CoL(1)-H2O](+) owing to the description of [Co2L(2)-2H2O](2+) as two non-interacting oxidized Co salen complexes bound via the central phenylene linker. Interestingly, TD-DFT calculations predict two electronic transitions that are 353 cm(-1) apart. The NIR spectrum of the analogous Ni complex, [Ni2L(2)](2+), exhibits two intense transitions (4890 cm(-1)/26 500 M(-1) cm(-1) and 4200 cm(-1)/21 200 M(-1) cm(-1)) due to exciton coupling in the excited state. Only one broad band is observed in the NIR spectrum for [Co2L(2)-2H2O](2+) as a result of the contracted donor and acceptor orbitals and overall CT character.