A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time-Resolved Luminescence Studies

Covalent hits and where to find them

Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.

Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase

Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1.78 and 1.61 Å resolution, respectively. It is also shown that despite coordinating a single non-natural metal cation, the PTE-R18 mutant is still able to maintain esterase activity.

Hybrid DFT Geometries and Properties for 17k Lanthanoid Complexes─The LnQM Data Set

The unique properties of lanthanoids and their diverse applications make them an indispensable part of modern research and industry. While the field has garnered attention, there remains a gap in available molecule data sets that facilitate both classical quantum chemistry calculations and the burgeoning field of machine learning in data science applications. This research addresses the need for a comprehensive data set that allows for a comparative analysis of various lanthanoids. The herein presented, curated data set includes 17269 monolanthanoid complexes derived from 1205 distinct ligand motifs. Structures encompass all 15 lanthanoids in the +3 oxidation state and exhibit molecular charges ranging from -1 to +3, including structures with a high spin multiplicity up to 8. Starting from lanthanum complexes, samples were processed with a permutation of the central lanthanoid atom, resulting in highly comparable subsets, facilitating comparative studies in which the influence of the lanthanoid can be investigated independently of ligand effects. The data set provides a broad range of features such as PBE0-D4/def2-SVP optimized geometries and optimization trajectories, while also covering ωB97M-V/def2-SVPD energies, rotational constants, dipole moments, highest occupied molecular orbital-lowest-unoccupied molecular orbital (HOMO-LUMO) energies, and Mulliken, Löwdin, and Hirshfeld population analyses. Additionally, coordination numbers, polarizabilities, and partial charges from D4, electronegativity equilibration (EEQ), GFN2-xTB, and charge extended Hückel (CEH) calculations are included. The data set is openly accessible and may serve as a basis for further investigations into the properties of lanthanoids.

Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center

The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed Cα/C' connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized 13C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of Cα and C' nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe2S2]+ clusters containing NEET protein CISD3 and the one [Fe4S4]2+ cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.

Validation of a post-radiolabeling bioconjugation strategy for radioactive rare earth complexes with minimal structural footprint

The nine-coordinate aza-macrocycle DO3Apic-NO2 and its kinetically inert rare earth complexes [M(DO3A-pic-NO2)]- (M = La, Tb, Eu, Lu, Y) can be readily bioconjugated to surface accessible thioles on peptides and proteins with a minimal structural footprint. All complexes express thioconjugation rate constants in the same order of magnitude (k = 0.3 h^-1) with the exception of Sc (k = 0.89 h^-1). Coupling to peptides and biologics with accessible cysteines also enables post-radiochelation bioconjugation at room temperature to afford injection-ready radiopharmaceuticals as demonstrated by formation of [¹⁷⁷Lu][Lu(DO3Apic-NO2)]^- and [⁸⁶Y][Y(DO3Apic-NO2)]^-, followed by post-labeling conjugation to a cysteine-functionalized peptide targeting the prostate specific membrane antigen. The ⁸⁶Y-labeled construct efficiently localizes in target tumors with no significant off-target accumulation as evidenced by positron emission tomography, biodistribution studies and metabolite analysis.

Increasing the Modulation Depth of GdIII-Based Pulsed Dipolar EPR Spectroscopy (PDS) with Porphyrin-GdIII Laser-Induced Magnetic Dipole Spectroscopy

Distance determination with pulsed EPR has become an important technique for the structural investigation of biomacromolecules, with double electron-electron resonance spectroscopy (DEER) as the most important method. Gd^III-based spin labels are one of the most frequently used spin labels for DEER owing to their stability against reduction, high magnetic moment, and absence of orientation selection. A disadvantage of Gd^III-Gd^III DEER is the low modulation depth due to the broad EPR spectrum of Gd^III. Here, we introduce laser-induced magnetic dipole spectroscopy (LaserIMD) with a spin pair consisting of Gd^III(PymiMTA) and a photoexcited porphyrin as an alternative technique. We show that the excited state of the porphyrin is not disturbed by the presence of the Gd^III complex and that herewith modulation depths of almost 40% are possible. This is significantly higher than the value of 7.2% that was achieved with Gd^III-Gd^III DEER.

Structure Determination of Binuclear Triple-Decker Phthalocyaninato Complexes by NMR via Paramagnetic Shifts Analysis Using Symmetry Peculiarities

The detailed knowledge about the structure of multinuclear paramagnetic lanthanide complexes for the targeted design of these compounds with special magnetic, sensory, optical and electronic properties is a very important task. At the same time, establishing the structure of such multinuclear paramagnetic lanthanide complexes in solution, using NMR is a difficult task, since several paramagnetic centers act simultaneously on the resulting chemical shift of a particular nucleus. In this paper, we have demonstrated the possibility of molecular structure determination in solution on the example of binuclear triple-decker lanthanide(III) complexes with tetra-15-crown-5-phthalocyanine Ln₂[(15C5)₄Pc]₃ {where Ln = Tb (1) and Dy (2)} by quantitative analysis of the pseudo-contact lanthanide-induced shifts (LIS). The symmetry of complexes was used for the simplification of the calculation of pseudo-contact shifts on the base of the expression for the magnetic susceptibility tensor in the arbitrary oriented magnetic axis system. Good agreement between the calculated and experimental shifts in the ¹H NMR spectra indicates the similarity of the structure for the complexes 1 and 2 in solution of CDCl₃ and the structure in the crystalline phase, found from the data of the X-ray structural study of the similar complex Lu₂[(15C5)₄Pc]₃. The described approach can be useful for LIS analysis of other polynuclear symmetric lanthanide complexes.

Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine

The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag for selective reaction with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between the lanthanoid ion and the protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP); (ii) reaction of the cyano groups with α -cysteine, penicillamine or β -cysteine to complete the lanthanoid chelating moiety; and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb 3 + and Tm 3 + ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-aminothiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron-electron resonance experiments after titration with Gd 3 +  ions.

Time-Resolved Luminescent Sensing and Imaging for Enzyme Catalytic Activity Based on Responsive Probes

Enzymes, as a kind of biomacromolecules, play an important role in many physiological processes and relate directly to various diseases. Developing an efficient detection method for enzyme activity is important to achieve early diagnosis of enzyme-relevant diseases and high throughput screening of potential enzyme-relevant drugs. Time-resolved luminescence assay provide a high accuracy and signal-to-noise ratios detection methods for enzyme activity, which has been widely used in high throughput screening of enzyme-relevant drugs and diagnosis of enzyme-relevant diseases. Inspired by these advantages, various responsive probes based on metal complexes and metal-free organic compounds have been developed for time-resolved bioimaging and biosensing of enzyme activity owing to their long luminescence lifetimes, high quantum yields and photostability. In this review, we comprehensively reviewed metal complex- and metal-free organic compound-based responsive probes applied to detect enzyme activity through time-resolved imaging, including their design strategies and sensing principles. Current challenges and future prospects in this rapidly growing field are also discussed.

Comparative Analysis of Mononuclear 1:1 and 2:1 Tetravalent Actinide (U, Th, Np) Complexes: Crystal Structure, Spectroscopy, and Electrochemistry

Six mononuclear tetravalent actinide complexes (1-6) have been synthesized using a new Schiff base ligand 2-methoxy-6-(((2-methyl-1-(pyridin-2-yl)propyl)imino)methyl)phenol (HL^pr). The HL^pr is treated with tetravalent actinide elements in varied stoichiometries to afford mononuclear 1:1 complexes [MCl₃-L^pr·nTHF] (1-3) and 2:1 complexes [MCl₂-L₂^pr] (4-6) (M = Th⁴⁺ (1 and 4), U⁴⁺ (2 and 5), and Np⁴⁺ (3 and 6)). All complexes are characterized using different analytical techniques such as IR, NMR, and absorption spectroscopy as well as crystallography. UV-vis spectroscopy revealed more red-shifted absorption spectra for 2:1 complexes as compared to 1:1 complexes. ¹H NMR of Th(IV) complexes exhibit diamagnetic spectra, whereas U(IV) and Np(IV) complexes revealed paramagnetically shifted ¹H NMR. Interestingly, NMR signals are paramagnetically shifted between -70 and 40 ppm in 2 and 3 but are confined within -35 to 25 ppm in 2:1 complexes 5 and 6. Single-crystal structures for 1:1 complexes revealed an eight-coordinated Th(IV) complex (1) and seven-coordinated U(IV) (2) and Np(IV) (3) complexes. However, all 2:1 complexes 4-6 were isolated as eight-coordinated isostructural molecules. The geometry around the Th⁴⁺ center in 1 is found to be trigonal dodecahedral and capped trigonal prismatic around U(IV) and Np(IV) centers in 2 and 3, respectively. However, An⁴⁺ centers in 2:1 complexes are present in dodecahedral geometry. Importantly, 2:1 complexes exhibit increased bond distances in comparison to their 1:1 counterparts as well as interesting bond modulation with respect to ionic radii of An(IV) centers. Cyclic voltammetry displays an increased oxidation potential of the ligand by 300-500 mV, after coordination with An⁴⁺. CV studies indicate Th(IV)/Th(II) reduction beyond -2.3 V, whereas attempts were made to identify redox potentials for U(IV) and Np(IV) centers. Spectroscopic binding studies reveal that complex stability in 1:1 stoichiometry follows the order Th⁴⁺ ≈ U⁴⁺ > Np⁴⁺.

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

Localising nuclear spins by pseudocontact shifts from a single tagging site

Ligating a protein at a specific site with a tag molecule containing a paramagnetic metal ion provides a versatile way of generating pseudocontact shifts (PCSs) in nuclear magnetic resonance (NMR) spectra. PCSs can be observed for nuclear spins far from the tagging site, and PCSs generated from multiple tagging sites have been shown to enable highly accurate structure determinations at specific sites of interest, even when using flexible tags, provided the fitted effective magnetic susceptibility anisotropy (Δ χ ) tensors accurately back-calculate the experimental PCSs measured in the immediate vicinity of the site of interest. The present work investigates the situation where only the local structure of a protein region or bound ligand is to be determined rather than the structure of the entire molecular system. In this case, the need for gathering structural information from tags deployed at multiple sites may be queried. Our study presents a computational simulation of the structural information available from samples produced with single tags attached at up to six different sites, up to six different tags attached to a single site, and in-between scenarios. The results indicate that the number of tags is more important than the number of tagging sites. This has important practical implications, as it is much easier to identify a single site that is suitable for tagging than multiple ones. In an initial experimental demonstration with the ubiquitin mutant S57C, PCSs generated with four different tags at a single site are shown to accurately pinpoint the location of amide protons in different segments of the protein.

Pseudocontact Shifts in Biomolecular NMR Spectroscopy

Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.

Localising individual atoms of tryptophan side chains in the metallo-β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

The metallo-β -lactamase IMP-1 features a flexible loop near the active site that assumes different conformations in single crystal structures, which may assist in substrate binding and enzymatic activity. To probe the position of this loop, we labelled the tryptophan residues of IMP-1 with 7-13 C-indole and the protein with lanthanoid tags at three different sites. The magnetic susceptibility anisotropy (Δ χ ) tensors were determined by measuring pseudocontact shifts (PCSs) of backbone amide protons. The Δ χ tensors were subsequently used to identify the atomic coordinates of the tryptophan side chains in the protein. The PCSs were sufficient to determine the location of Trp28, which is in the active site loop targeted by our experiments, with high accuracy. Its average atomic coordinates showed barely significant changes in response to the inhibitor captopril. It was found that localisation spaces could be defined with better accuracy by including only the PCSs of a single paramagnetic lanthanoid ion for each tag and tagging site. The effect was attributed to the shallow angle with which PCS isosurfaces tend to intersect if generated by tags and tagging sites that are identical except for the paramagnetic lanthanoid ion.

Versatile Para-Substituted Pyridine Lanthanide Coordination Complexes Allow Late Stage Tailoring of Complex Function

A series of cationic and neutral p-Br and p-NO2 pyridine substituted Eu(III) and Gd(III) coordination complexes serve as versatile synthetic intermediates. Nucleophilic aromatic substitution occurs readily at the para position under mild conditions, allowing C-N and C-C bond forming reactions to take place, permitting the introduction of azide, amino and alkynyl substituents. For Eu(III) complexes, this approach allows late stage tuning of absorption and emission spectral properties, exemplified by the lowering of the energy of an LMCT transition accompanied by a reduction in the Eu-Npy bond length. Additionally, these complexes provide direct access to the corresponding Eu(II) analogues. With the Gd(III) series, the nature of the p-substituent does not significantly change the EPR properties (linewidth, relaxation times), as required for their development as EPR spin probes that can be readily conjugated to biomolecules under mild conditions.