Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development.

Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.

The interoperability of crystallographic data and databases.

Interoperability of crystallographic data with other disciplines is essential for the smooth and rapid progress of structure-based science in the computer age. Within crystallography and closely related subject areas, there is already a high level of conformance to the generally accepted FAIR principles (that data be findable, accessible, interoperable and reusable) through the adoption of common information exchange protocols by databases, publishers, instrument vendors, experimental facilities and software authors. Driven by the success within these domains, the IUCr has worked closely with CODATA (the Committee on Data of the International Science Council) to help develop the latter's commitment to cross-domain integration of discipline-specific data. The IUCr has, in particular, emphasized the need for standards relating to data quality and completeness as an adjunct to the FAIR data landscape. This can ensure definitive reusable data, which in turn can aid interoperability across domains. A microsymposium at the IUCr 2023 Congress provided an up-to-date survey of data interoperability within and outside of crystallography, expounded using a broad range of examples.

(N-Benzoyl-N-phenyl-hydroxy-laminato)carbon-yl(tri-phenyl-arsine)rhodium(I).

The mol-ecule of the title compound, [Rh(C13H10NO2){As(C6H5)3}(CO)] or [Rh(BPHA)(AsPh3)(CO)] (BPHA is the N-benzoyl-N-phenyl-hydroxy-laminate anion), comprises a bidentate N-benzoyl-N-phenyl-hydroxy-laminate anion coordinating through the O atoms to the soft Lewis acid, rhodium(I), and two monodentate ligands, viz. tri-phenyl-arsine and carbonyl. The resulting CO2As coordination environment around the central RhI atom is distorted square planar.=.

Trends in coordination of rhenium organometallic complexes in the Protein Data Bank.

Radiopharmaceutical development has similar overall characteristics to any biomedical drug development requiring a compound's stability, aqueous solubility and selectivity to a specific disease site. However, organometallic complexes containing 188/186Re or 99mTc involve a d-block transition-metal radioactive isotope and therefore bring additional factors such as metal oxidation states, isotope purity and half life into play. This topical review is focused on the development of radiopharmaceuticals containing the radioisotopes of rhenium and technetium and, therefore, on the occurrence of these organometallic complexes in protein structures in the Worldwide Protein Data Bank (wwPDB). The purpose of incorporating the group 7 transition metals of rhenium/technetium in the protein and the reasons for study by protein crystallography are described, as certain PDB studies were not aimed at drug development. Technetium is used as a medical diagnostic agent and involves the 99mTc isotope which decays to release gamma radiation, thereby employed for its use in gamma imaging. Due to the periodic relationship among group 7 transition metals, the coordination chemistry of rhenium is similar (but not identical) to that of technetium. The types of reactions the potential model radiopharmaceutical would prefer to partake in, and by extension knowing which proteins and biomolecules the compound would react with in vivo, are needed. Crystallography studies, both small molecule and macromolecular, are a key aspect in understanding chemical coordination. Analyses of bonding modes, coordination to particular residues and crystallization conditions are presented. In our Forward look as a concluding summary of this topical review, the question we ask is: what is the best way for this field to progress?

New approach for the synthesis of water soluble fac-[MI(CO)3]+ bis(diarylphosphino)alkylamine complexes (M = 99Tc, Re).

A novel proof-of-concept is reported to modify the water solubility and potential biological effects of a bis(diphenylphosphino)alkylamine (PNP) ligand and the corresponding metal complex, by introducing an amine group on the outer periphery of the pendant ligand arm. Thus, a tertiary butoxycarbonyl protected N'-Boc-ethylenediamine-N,N-bis(diphenylphosphino) (N'-Boc-PNP) ligand (1) was synthesized by reacting the protected ethylenediamine and chlorodiphenylphosphine in a 1 : 2 molar ratio. The corresponding fac-[Re(CO)3(N'-Boc-PNP)Br] (1A) complex was then obtained by reacting N'-Boc-PNP (1) with (Et4N)2fac-[Re(CO)3Br3] in equimolar amounts in DCM at 50 °C. De-protection of the N'-Boc pendant amine group in 1A with TFA leads to fac-[Re(NH3+-PNP)(CO)3Br]·CF3COO- (1B) which is soluble in D2O (>0.05 M). Treating 1B with saturated aqueous NaHCO3 yields fac-[Re(NH2-PNP)(CO)3Br]·MeOH (1C) in near quantitative yield. Although both 1A and 1C are not soluble in D2O, addition of TFA easily generates 1B (31P NMR), confirming the formation of the protonated amine. Isolation of fac-[99Tc(CO)3(N-Boc-PNP)(Cl)] (1D) confirmed that the rhenium and technetium (99Tc) can be easily interchanged in this process. Reported are hence the unique rhenium series of compounds 1A, 1B and 1C and the corresponding technetium complex 1D, unequivocally characterized by single crystal XRD, as well as IR and 1H NMR spectroscopy. Preliminary antimicrobial evaluation indicates that ligand 1 and its respective rhenium complexes (1A-1C) were not active against selected fungi (Candida albicans and Cryptococcus neoformans) and bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus). These types of ligands and complexes therefore present themselves as excellent radio models for further evaluation using 186Re, 188Re and 99mTc to potentially study the radiotoxicity of appropriately designed complexes.

Substitution reactivity and structural variability induced by tryptamine on the biomimetic rhenium tricarbonyl complex.

A series of seven fac-[Re(CO)3(5Me-Sal-Trypt)(L)] complexes containing tryptamine on the N,O 5-methyl-salicylidene bidentate ligand backbone and where L is MeOH, Py, Imi, DMAP, PPh3 coordinated to the 6th position have been studied, including the formation of a dinuclear Re2 cluster. The crystallographic solid state structures show marked similarity in structural tendency, in particular the rigidity of the Re core and the hydrogen bond interactions similar to those found in protein structures. The rates of formation and stability of the complexes were evaluated by rapid time-resolved stopped-flow techniques and the methanol substitution reaction indicates the significant activation induced by the use of the N,O salicylidene bidentate ligand as manifested by the second-order rate constants for the entering nucleophiles. Both linear and limiting kinetics were observed and a systematic evaluation of the kinetics is reported clearly indicating an interchange type of intimate mechanism for the methanol substitution. The anticancer activity of compounds 1-7 was tested on HeLa cells and it was found that all compounds showed similar cytotoxicity where solubility allowed. IC50-values between ca. 11 and 22 µM indicate that some cytotoxicity resides most likely on the salicylidene-tryptamine ligand. The photoluminescence of the seven complexes is similar in maximum emission wavelength with little variation despite the broad range of ligands coordinated to the 6th position on the metal centre.

Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult?

The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins.

Symmetry correlations between crystallographic and photoluminescence study of ternary ß-diketone europium(iii) based complexes using 1,10-phenanthroline as the ancillary ligand.

This work entails deep red emitting EuIII based complexes with a variety of ternary ß-diketonate ligands and 1,10-phenanthroline as the ancillary ligand in the system. The solid state structure and spectroscopic analysis has been outlaid in terms of photoluminescence and crystallography. A luminescence quantum efficiency of 50% was obtained for the [tris-(4,4,4-trifluoro-1-chlorophenyl-butanedione)mono-(1,10-phenanthroline)europium(iii)] complexes. Moreover, complexes [tris-(2,2,6,6-tetramethyl-heptanedione)mono-(1,10-phenanthroline) europium(iii)] and {[hexa-(benzyl carboxylic acid) bis-(1,10-phenanthroline)di-europium(iii)]-µ-[κ2-O,O'-(benzyl carboxylic acid)]2} were found to also have quantum yields of 9% and 28% with respective sensitization efficiencies of 85%, 15% and 58%. These results were articulated with crystallographic details pertaining to the nature of coordination and the effect of steric and electronic properties thereof which somewhat impacts the Eu-N bond distances. A symmetry correlation was drawn between the crystallographic data and the photoluminescence data.

Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging.

The fact that a protein crystal can serve as a chemical reaction vessel is intrinsically fascinating. That it can produce an electron-dense tetranuclear rhenium cluster compound from a rhenium tri-carbonyl tri-bromo starting compound adds to the fascination. Such a cluster has been synthesized previously in vitro, where it formed under basic conditions. Therefore, its synthesis in a protein crystal grown at pH 4.5 is even more unexpected. The X-ray crystal structures presented here are for the protein hen egg-white lysozyme incubated with a rhenium tri-carbonyl tri-bromo compound for periods of one and two years. These reveal a completed, very well resolved, tetra-rhenium cluster after two years and an intermediate state, where the carbonyl ligands to the rhenium cluster are not yet clearly resolved, after one year. A dense tetranuclear rhenium cluster, and its technetium form, offer enhanced contrast in medical imaging. Stimulated by these crystallography results, the unusual formation of such a species directly in an in vivo situation has been considered. It offers a new option for medical imaging compounds, particularly when considering the application of the pre-formed tetranuclear cluster, suggesting that it may be suitable for medical diagnosis because of its stability, preference of formation and biological compatibility.

Synthesis of ReI tricarbonyl complexes with various sulfur- and oxygen-donating ligands: crystal structures of two ReI dinuclear structures bridged by S atoms.

The synthesis and characterization of two dinuclear complexes, namely fac-hexacarbonyl-1κ3C,2κ3C-(pyridine-1κN)[µ-2,2'-sulfanediyldi(ethanethiolato)-1κ2S1,S3:2κ3S1,S2,S3]dirhenium(I), [Re2(C4H8S3)(C5H5N)(CO)6], (1), and tetraethylammonium fac-tris(µ-2-methoxybenzenethiolato-κ2S:S)bis[tricarbonylrhenium(I)], (C8H20N)[Re2(C7H7OS)3(CO)6], (2), together with two mononuclear complexes, namely (2,2'-bithiophene-5-carboxylic acid-κ2S,S')bromidotricarbonylrhenium(I), (3), and bromidotricarbonyl(methyl benzo[b]thiophene-2-carboxylate-κ2O,S)rhenium(I), (4), are reported. Crystals of (1) and (2) were characterized by X-ray diffraction. The crystal structure of (1) revealed two Re-S-Re bridges. The thioether S atom only bonds to one of the ReI metal centres, while the geometry of the second ReI metal centre is completed by a pyridine ligand. The structure of (2) is characterized by three S-atom bridges and an Re...Re nonbonding distance of 3.4879 (5) Å, which is shorter than the distance found for (1) [3.7996 (6)/3.7963 (6) Å], but still clearly a nonbonding distance. Complex (1) is stabilized by six intermolecular hydrogen-bond interactions and an O...O interaction, while (2) is stabilized by two intermolecular hydrogen-bond interactions and two O...π interactions.

Self-Assembled Multinuclear Complexes Incorporating 99m Tc.

Multinuclear complexes or clusters are rarely investigated in medicinal inorganic chemistry although they represent structural intermediates between molecules and nanomaterials. We present in this report two strategies towards 99m Tc-containing clusters. In a pre-assembly approach, the preformed but incomplete cluster fragment [Re3 (µ2 -OH)3 (µ3 -OH)(CO)9 ]- reacts with [99m Tc(CO)3 ]+ to the highly stable [99m TcRe3 (µ3 -OH)4 (CO)12 ] cube. The same structure self-assembles when reacting the mononuclear Re and 99m Tc precursors in one pot. Integrating the coordinating OH groups from Schiff bases in this concept leads straight to dinuclear, mixed-metal complexes of the type [99m TcRe(µ2 -O^N-R1 )2 (CO)6 ] in quantitative yields. Both strategies are unprecedented and open a future path towards clusters, incorporating a 99m Tc radiolabel while being decorated with targeting or cytotoxic moieties.

Crystal structure of (E)-4-benzyl-idene-6-phenyl-1,2,3,4,7,8,9,10-octa-hydro-phenanthridine.

The preparation of the title compound, C26H25N, was achieved by the condensation of an ethano-lic mixture of benzaldehyde, cyclo-hexa-none and ammonium acetate in a 2:1:1 molar ratio. There are two crystallographically independent mol-ecules in the asymmetric unit. The two cyclo-hexyl rings adopt an anti-envelope conformation with the benzyl moiety adopting a cis conformation with respect to the nitro-gen atom of the phenanthridine segment. In the crystal, mol-ecules are linked through C-H⋯N inter-actions into hydrogen-bonded chains that are further arranged into distinct layers by weak offset π-π inter-actions.

New leads for fragment-based design of rhenium/technetium radiopharmaceutical agents.

Multiple possibilities for the coordination of fac-[Re(CO)3(H2O)3]+ to a protein have been determined and include binding to Asp, Glu, Arg and His amino-acid residues as well as to the C-terminal carboxylate in the vicinity of Leu and Pro. The large number of rhenium metal complex binding sites that have been identified on specific residues thereby allow increased target identification for the design of future radiopharmaceuticals. The core experimental concept involved the use of state-of-art tuneable synchrotron radiation at the Diamond Light Source to optimize the rhenium anomalous dispersion signal to a large value (f'' of 12.1 electrons) at its LI absorption edge with a selected X-ray wavelength of 0.9763 Å. At the Cu Kα X-ray wavelength (1.5418 Å) the f'' for rhenium is 5.9 electrons. The expected peak-height increase owing to the optimization of the Re f'' was therefore 2.1. This X-ray wavelength tuning methodology thereby showed the lower occupancy rhenium binding sites as well as the occupancies of the higher occupancy rhenium binding sites.

Structural comparison of group 7 tricarbonyl complexes of 2-{[2-(1H-imidazol-4-yl)ethyl]iminomethyl}-5-methylphenolate.

Two tricarbonyl complexes of rhenium(I) and manganese(I) coordinated by the ligand 2-{[2-(1H-imidazol-4-yl)ethyl]iminomethyl}-5-methylphenolate are reported, viz. fac-tricarbonyl(2-{[2-(1H-imidazol-4-yl-κN(3))ethyl]iminomethyl-κN}-5-methylphenolato-κO)rhenium(I) methanol monosolvate, [Re(C16H14N3O4)(CO)3]·CH3OH, (I), and fac-tricarbonyl(2-{[2-(1H-imidazol-4-yl-κN(3))ethyl]iminomethyl-κN}-5-methylphenolato-κO)manganese(I), fac-[Mn(C16H14N3O4)(CO)3], (II), display facial coordination in a distorted octahedral environment. The crystal structure of (I) is stabilized by O-H···O, N-H···O and C-H···O hydrogen-bond interactions, while that of (II) is stabilized by N-H...O hydrogen-bond interactions only. These interactions result in two-dimensional networks and π-π stacking for both structures.

X-ray diffraction in temporally and spatially resolved biomolecular science.

Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a 'crystal lattice free' single molecule, with or without temporal resolved structural changes. This is altogether very challenging R&D. So as to assist this effort we have undertaken studies of metal clusters that bind to proteins, both 'fresh' and after repeated X-ray irradiation to assess their X-ray-photo-dynamics, namely Ta6Br12, K2PtI6 and K2PtBr6 bound to a test protein, hen egg white lysozyme. These metal complexes have the major advantage of being very recognisable shapes (pseudo spherical or octahedral) and thereby offer a start to (probably very difficult) single molecule electron density map interpretations, both static and dynamic. A further approach is to investigate the X-ray laser beam diffraction strength of a well scattering nano-cluster; an example from nature being the iron containing ferritin. Electron crystallography and single particle electron microscopy imaging offers alternatives to X-ray structural studies; our structural studies of crustacyanin, a 320 kDa protein carotenoid complex, can be extended either by electron based techniques or with the X-ray laser representing a fascinating range of options. General outlook remarks concerning X-ray, electron and neutron macromolecular crystallography as well as 'NMR crystallography' conclude the article.

Solid state isostructural behavior and quantified limiting substitution kinetics in Schiff-base bidentate ligand complexes fac-[Re(O,N-Bid)(CO)3(MeOH)](n).

A range of N,O-donor atom salicylidene complexes of the type fac-[M(O,N-Bid)(CO)3(L)](n) (O,N-Bid = anionic N,O-bidentate ligands; L = neutral coordinated ligand) have been studied. The unique feature of the complexes which crystallize in a monoclinic isostructural space group for complexes containing methanol in the sixth position (L = MeOH) is highlighted. The reactivity and stability of the complexes were evaluated by rapid stopped-flow techniques, and the methanol substitution by a range of pyridine type ligands indicates significant activation by the N,O-salicylidene type of bidentate ligands as observed from the variation in the second-order rate constants. In particular, following the introduction of the sterically demanding and electron rich cyclohexyl salicylidene moiety on the bidentate ligand, novel limiting kinetic behavior is displayed by all entering ligands, thus enabling a systematic probe and manipulation of the limiting kinetic constants. Clear evidence of an interchange type of intimate mechanism for the methanol substitution is produced. The equilibrium and rate constants (25 °C) for the two steps in the dissociative interchange mechanism for methanol substitution in fac-[Re(Sal-Cy)(CO)3(MeOH)] (5) by the pyridine type ligands 3-chloropyridine, pyridine, 4-picoline, and DMAP are k3 (s(-1)), 40 ± 4, 13 ± 2, 10.4 ± 0.7, and 2.11 ± 0.09, and K2 (M(-1)), 0.13 ± 0.01, 0.21 ± 0.03, 0.26 ± 0.02, and 1.8 ± 0.1, respectively.

Fast and reversible insertion of carbon dioxide into zirconocene-alkoxide bonds. A mechanistic study.

In two consecutive equilibria the compound (Cp*)2Zr(OMe)2 undergoes insertion of CO2 to form the mono- and bis-hemicarbonates. Both equilibria are exothermic but entropically disfavoured. Magnetisation transfer experiments gave kinetic data for the first equilibrium showing that the rate of insertion is overall second order with a rate constant of 3.20 ± 0.12 M(-1) s(-1), which is substantially higher than those reported for other early transition metal alkoxides, which are currently the best homogeneous catalysts for dimethyl carbonate formation from methanol and CO2. Activation parameters for the insertion reaction point to a highly ordered transition state and we interpret that as there being a substantial interaction between the CO2 and the metal during the C-O bond formation. This is supported by DFT calculations showing the lateral attack by CO2 to have the lowest energy transition state.

Activation of rhenium(I) toward substitution in fac-[Re(N,O'-Bid)(CO)3(HOCH3)] by Schiff-base bidentate ligands (N,O'-Bid).

A series of fac-[Re(N,O'-Bid)(CO)3(L)] (N,O'-Bid = monoanionic bidentate Schiff-base ligands with N,O donor atoms; L = neutral monodentate ligand) has been synthesized, and the methanol substitution reactions have been investigated. The complexes were characterized by NMR, IR, and UV-vis spectroscopy. X-ray crystal structures of the compounds fac-[Re(Sal-mTol)(CO)3(HOCH3)], fac-[Re(Sal-pTol)(CO)3(HOCH3)], fac-[Re(Sal-Ph)(CO)3(HOCH3)], and fac-[Re(Sal-Ph)(CO)3(Py)] (Sal-mTol = 2-(m-tolyliminomethyl)phenolato; Sal-pTol = 2-(p-tolyliminomethyl)phenolato; Sal-Ph = 2-(phenyliminomethyl)phenolato; Py = pyridine) are reported. Significant activation for the methanol substitution is induced by the use of the N,O bidentate ligand as manifested by the second order rate constants, with limiting kinetics being observed for the first time. Rate constants (25 °C) (k1 or k3) and activation parameters (ΔHk‡, kJ mol(-1); ΔSk‡, J K(-1) mol(-1)) from Eyring plots for entering nucleophiles as indicated are as follows: fac-[Re(Sal-mTol)(CO)3(HOCH3)] 3-chloropyridine: (k1) 2.33 ± 0.01 M(-1) s(-1); 85.1 ± 0.6, 48 ± 2; fac-[Re(Sal-mTol)(CO)3(HOCH3)] pyridine: (k1) 1.29 ± 0.02 M(-1) s(-1); 92 ± 2, 66 ± 7; fac-[Re(Sal-mTol)(CO)3(HOCH3)] 4-picoline: (k1) 1.27 ± 0.05 M(-1) s(-1); 88 ± 2, 53 ± 6; (k3) 3.9 ± 0.03 s(-1); 78 ± 8, 30 ± 27; (kf) 1.7 ± 0.02 M(-1) s(-1); 86 ± 2, 49 ± 6; fac-[Re(Sal-mTol)(CO)3(HOCH3)] DMAP (k3) 1.15 ± 0.02 s(-1); 88 ± 2, 52 ± 7. An interchange dissociative mechanism is proposed.

4-Fluoro-2-[(3-methyl-phen-yl)imino-meth-yl]phenol.

The title compound, C(14)H(12)FNO, crystallizes as the trans phenol-imine tautomer. The two benzene rings are essentially coplanar, being inclined to one another by 9.28 (7)°. This is at least in part due to the intra-molecular O-H⋯N hydrogen bond between the hy-droxy O atom and the imine N atom. The crystal structure is stabilized by an array of weak C-H⋯O and C-H⋯F inter-actions, which link the mol-ecules into a stable three-dimensional network.

4-(2-Chloro-phenyl-amino)-pent-3-en-2-one.

In the title compound, C(11)H(12)ClNO, intra-molecular N-H⋯O hydrogen bonding is present. The dihedral angle between the benzene ring and the pentenone unit is 46.52 (5)°. In the crystal, C-H⋯O inter-actions between hydrogen atoms of the aryl moiety and two separate oxygen atoms occur, leading to a three-dimensional network.