A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe

54 K Spin Transition Temperature Shift in a Fe6L4 Octahedral Cage Induced by Optimal Fitted Multiple Guests

Spin-crossover (SCO) coordination cages are at the forefront of research for their potential in crafting next-generation molecular devices. However, due to the scarcity of SCO hosts and their own limited cavities, the interplay between the SCO host and the multiple guests binding has remained elusive. In this contribution, we present a family of pseudo-octahedral coordination cages (M6L4, M = ZnII, CoII, FeII, and NiII) assembled from a tritopic tridentate ligand L with metal ions. The utilization of FeII ion leads to the successful creation of the Fe6L4-type SCO cage. Host-guest studies of these M6L4 cages reveal their capacity to encapsulate four adamantine-based guests. Notably, the spin transition temperature T1/2 of Fe6L4 is dependent on the multiple guests encapsulated. The inclusion of adamantine yields an unprecedented T1/2 shift of 54 K, a record shift in guest-mediated SCO coordination cages to date. This drastic shift is ascribed to the synergistic effect of multiple guests coupled with their optimal fit within the host. Through a straightforward thermodynamic cycle, the binding affinities of the high-spin (HS) and low-spin (LS) states are separated from their apparent binding constant. This result indicates that the LS state has a stronger binding affinity for the multiple guests than the HS state. Exploring the SCO thermodynamics of host-guest complexes allows us to examine the optimal fit of multiple guests to the host cavity. This study reveals that the T1/2 of the SCO host can be manipulated by the encapsulation of multiple guests, and the SCO cage is an ideal candidate for determining the multiple guest fit.

Metalation of a Hierarchical Self-Assembly Consisting of π-Stacked Cubes through Single-Crystal-to-Single-Crystal Transformation

Single-crystal-to-single-crystal metalation of organic ligands represents a novel method to prepare metal-organic complexes, but remains challenging. Herein, a hierarchical self-assembly {(H₁₂L₈)·([N(C₂H₅)₄]⁺)₃·(ClO₄^-)₁₅·(H₂O)₃₂} (1) (L = tris(2-benzimidazolylmethyl) amine) consisting of π-stacked cubes which are assembled from eight partially protonated L ligands is obtained. By soaking the crystals of compound 1 in the aqueous solution of Co(SCN)₂, the ligands coordinate with Co²⁺ ions stoichiometrically and ClO₄^- exchange with SCN^- via single-crystal-to-single-crystal transformation, leading to {([CoSCNL]⁺)₈·([NC₈H₂₀]⁺)₃·(SCN)₁₁·(H₂O)₁₃} (2).

Rigidified and Hydrophilic DOTA-like Lanthanoid Ligands: Design, Synthesis, and Dynamic Properties

Limiting the dynamics of paramagnetic tags is crucial for the accuracy of the structural information derived from paramagnetic nuclear magnetic resonance (NMR) experiments. A hydrophilic rigid 2,2',2″,2‴-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetraacetic acid (DOTA)-like lanthanoid complex was designed and synthesized following a strategy that allows the incorporation of two sets of two adjacent substituents. This resulted in a C₂ symmetric hydrophilic and rigid macrocyclic ring, featuring four chiral hydroxyl-methylene substituents. NMR spectroscopy was used to investigate the conformational dynamics of the novel macrocycle upon complexation with europium and compared to DOTA and its derivatives. The twisted square antiprismatic and square antiprismatic conformers coexist, but the former is favored, which is different from DOTA. Two-dimensional ¹H exchange spectroscopy shows that ring flipping of the cyclen-ring is suppressed due to the presence of the four chiral equatorial hydroxyl-methylene substituents at proximate positions. The reorientation of the pendant arms causes conformational exchange between two conformers. The reorientation of the coordination arms is slower when the ring flipping is suppressed. This indicates that these complexes are suitable scaffolds to develop rigid probes for paramagnetic NMR of proteins. Due to their hydrophilic nature, it is anticipated that they are less likely to cause protein precipitation than their more hydrophobic counterparts.

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.

Stable and inert macrocyclic cobalt(II) and nickel(II) complexes with paraCEST response

We report the synthesis of the macrocyclic ligands 3,9-PC2AMH (2,2'-(3,6,9-triaza-1(2,6)-pyridinacyclodecaphane-3,9-diyl)diacetamide) and 3,9-PC2AMtBu (2,2'-(3,6,9-triaza-1(2,6)-pyridinacyclodecaphane-3,9-diyl)bis(N-tert-butyl)acetamide) which contain a pyclen platform functionalized with acetamide or tert-butylacetamide pendant arms at positions 3 and 9 of the macrocyclic unit. The corresponding Co(II) and Ni(II) complexes were prepared, isolated and characterised as potential paramagnetic chemical exchange saturation transfer (paraCEST) agents. The X-ray structures of the Ni(II) complexes reveal six-coordination of the ligands to the metal ion. The Co(II) complex with 3,9-PC2AMtBu shows a similar six-coordinate structure in the solid state, while the Co(II) complex with 3,9-PC2AMH contains a seven-coordinate metal ion, seventh coordination being completed by the presence of an inner-sphere water molecule. The structure of the Co(II) complexes was investigated using ¹H NMR spectroscopy and computational methods. The complexes present a seven-coordinate structure in solution, as demonstrated by the analysis of the paramagnetic shifts using density functional theory. Ligand protonation constants and stability constants of the complexes with 3,9-PC2AMH were determined using potentiometric titrations (I = 0,15 M NaCl). The Co(II) complex was found to be more stable than the Ni(II) analogue (log K_CoL = 14.46(5) and log K_NiL = 13.15(3)). However, the Ni(II) and Co(II) complexes display similar rate constants characterizing the proton-assisted dissociation mechanism. The presence of highly shifted ¹H NMR signals due to the amide protons in slow exchange with bulk water results in sizeable CEST signals, which are observed at +67 and +15 ppm for the Co(II) complex with 3,9-PC2AMH and +42 and +7 ppm for the Ni(II) analogue at 25 °C.

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.

Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins

Linear polyubiquitin chains regulate diverse signaling proteins, in which the chains adopt various conformations to recognize different target proteins. Thus, the structural plasticity of the chains plays an important role in controlling the binding events. Herein, paramagnetic NMR spectroscopy is employed to explore the conformational space sampled by linear diubiquitin, a minimal unit of linear polyubiquitin, in its free state. Rigorous analysis of the data suggests that, regarding the relative positions of the ubiquitin units, particular regions of conformational space are preferentially sampled by the molecule. By combining these results with further data collected for charge-reversal derivatives of linear diubiquitin, structural insights into the factors underlying the binding events of linear diubiquitin are obtained.

Lipid-nanodiscs formed by paramagnetic metal chelated polymer for fast NMR data acquisition

Lipid-nanodiscs have been shown to be an exciting innovation as a membrane-mimicking system for studies on membrane proteins by a variety of biophysical techniques, including NMR spectroscopy. Although NMR spectroscopy is unique in enabling the atomic-resolution investigation of dynamic structures of membrane-associated molecules, it, unfortunately, suffers from intrinsically low sensitivity. The long data acquisition often used to enhance the sensitivity is not desirable for sensitive membrane proteins. Instead, paramagnetic relaxation enhancement (PRE) has been used to reduce NMR data acquisition time or to reduce the amount of sample required to acquire an NMR spectra. However, the PRE approach involves the introduction of external paramagnetic probes in the system, which can induce undesired changes in the sample and on the observed NMR spectra. For example, the addition of paramagnetic ions, as frequently used, can denature the protein via direct interaction and also through sample heating. In this study, we show how the introduction of paramagnetic tags on the outer belt of polymer-nanodiscs can be used to speed-up data acquisition by significantly reducing the spin-lattice relaxation (T1) times with minimum-to-no alteration of the spectral quality. Our results also demonstrate the feasibility of using different types of paramagnetic ions (Eu3+, Gd3+, Dy3+, Er3+, Yb3+) for NMR studies on lipid-nanodiscs. Experimental results characterizing the formation of lipid-nanodiscs by the metal-chelated polymer, and their increased tolerance toward metal ions are also reported.

Measuring transverse relaxation in highly paramagnetic systems

The enhancement of nuclear relaxation rates due to the interaction with a paramagnetic center (known as Paramagnetic Relaxation Enhancement) is a powerful source of structural and dynamics information, widely used in structural biology. However, many signals affected by the hyperfine interaction relax faster than the evolution periods of common NMR experiments and therefore they are broadened beyond detection. This gives rise to a so-called blind sphere around the paramagnetic center, which is a major limitation in the use of PREs. Reducing the blind sphere is extremely important in paramagnetic metalloproteins. The identification, characterization, and proper structural restraining of the first coordination sphere of the metal ion(s) and its immediate neighboring regions is key to understand their biological function. The novel HSQC scheme we propose here, that we termed R2-weighted, HSQC-AP, achieves this aim by detecting signals that escaped detection in a conventional HSQC experiment and provides fully reliable R2 values in the range of 1H R2 rates ca. 50-400 s-1. Independently on the type of paramagnetic center and on the size of the molecule, this experiment decreases the radius of the blind sphere and increases the number of detectable PREs. Here, we report the validation of this approach for the case of PioC, a small protein containing a high potential 4Fe-4S cluster in the reduced [Fe4S4]2+ form. The blind sphere was contracted to a minimal extent, enabling the measurement of R2 rates for the cluster coordinating residues.

Paramagnetic NMR in drug discovery

The presence of an unpaired electron in paramagnetic molecules generates significant effects in NMR spectra, which can be exploited to provide restraints complementary to those used in standard structure-calculation protocols. NMR already occupies a central position in drug discovery for its use in fragment screening, structural biology and validation of ligand-target interactions. Paramagnetic restraints provide unique opportunities, for example, for more sensitive screening to identify weaker-binding fragments. A key application of paramagnetic NMR in drug discovery, however, is to provide new structural restraints in cases where crystallography proves intractable. This is particularly important at early stages in drug-discovery programs where crystal structures of weakly-binding fragments are difficult to obtain and crystallization artefacts are probable, but structural information about ligand poses is crucial to guide medicinal chemistry. Numerous applications show the value of paramagnetic restraints to filter computational docking poses and to generate interaction models. Paramagnetic relaxation enhancements (PREs) generate a distance-dependent effect, while pseudo-contact shift (PCS) restraints provide both distance and angular information. Here, we review strategies for introducing paramagnetic centers and discuss examples that illustrate the utility of paramagnetic restraints in drug discovery. Combined with standard approaches, such as chemical shift perturbation and NOE-derived distance information, paramagnetic NMR promises a valuable source of information for many challenging drug-discovery programs.

The Photocatalyzed Thiol-ene reaction: A New Tag to Yield Fast, Selective and reversible Paramagnetic Tagging of Proteins

Paramagnetic restraints have been used in biomolecular NMR for the last three decades to elucidate and refine biomolecular structures, but also to characterize protein-ligand interactions. A common technique to generate such restraints in proteins, which do not naturally contain a (paramagnetic) metal, consists in the attachment to the protein of a lanthanide-binding-tag (LBT). In order to design such LBTs, it is important to consider the efficiency and stability of the conjugation, the geometry of the complex (conformational exchanges and coordination) and the chemical inertness of the ligand. Here we describe a photo-catalyzed thiol-ene reaction for the cysteine-selective paramagnetic tagging of proteins. As a model, we designed an LBT with a vinyl-pyridine moiety which was used to attach our tag to the protein GB1 in fast and irreversible fashion. Our tag T1 yields magnetic susceptibility tensors of significant size with different lanthanides and has been characterized using NMR and relaxometry measurements.

A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe

Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes. Herein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to a protein to generate a pseudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid‐based probes. The observed PCS are relatively small, making cobalt‐based probes suitable for localized studies, such as of an active site. The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages. The properties of TraNPs in comparison with other cobalt‐based probes are discussed.