Receptor‐Bound Conformation of Cilengitide Better Represented by Its Solution‐State Structure than the Solid‐State Structure

The X‐ray crystal and NMR spectroscopic structures of the peptide drug candidate Cilengitide (cyclo(RGDf(NMe)Val)) in various solvents are obtained and compared in addition to the integrin receptor bound conformation. The NMR‐based solution structures exhibit conformations closely resembling the X‐ray structure of Cilengitide bound to the head group of integrin αvβ3. In contrast, the structure of pure Cilengitide recrystallized from methanol reveals a different conformation controlled by the lattice forces of the crystal packing. Molecular modeling studies of the various ligand structures docked to the αvβ3 integrin revealed that utilization of the solid‐state conformation of Cilengitide leads—unlike the solution‐based structures—to a mismatch of the ligand–receptor interactions compared with the experimentally determined structure of the protein–ligand complex. Such discrepancies between solution and crystal conformations of ligands can be misleading during the structure‐based lead optimization process and should thus be taken carefully into account in ligand orientated drug design.     

Design and Synthesis of High‐Affinity Dimeric Inhibitors Targeting the Interactions between Gephyrin and Inhibitory Neurotransmitter Receptors

Gephyrin is the central scaffolding protein for inhibitory neurotransmitter receptors in the brain. Here we describe the development of dimeric peptides that inhibit the interaction between gephyrin and these receptors, a process which is fundamental to numerous synaptic functions and diseases of the brain. We first identified receptor‐derived minimal gephyrin‐binding peptides that displayed exclusive binding towards native gephyrin from brain lysates. We then designed and synthesized a series of dimeric ligands, which led to a remarkable 1220‐fold enhancement of the gephyrin affinity (K_D=6.8 nM ). In X‐ray crystal structures we visualized the simultaneous dimer‐to‐dimer binding in atomic detail, revealing compound‐specific binding modes. Thus, we defined the molecular basis of the affinity‐enhancing effect of multivalent gephyrin inhibitors and provide conceptually novel compounds with therapeutic potential, which will allow further elucidation of the gephyrin–receptor interplay.     

Intermolecular Interactions and Protein Dynamics by Solid‐State NMR Spectroscopy

Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1–antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site‐specific ¹⁵N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond–nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small‐amplitude overall anisotropic motion sampling the interaction interface in the complex.     

Full Characterization of Colloidal Solutions of Long‐Alkyl‐Chain‐Amine‐Stabilized ZnO Nanoparticles by NMR Spectroscopy: Surface State,Equilibria, and Affinity

Full NMR characterization of ZnO nanoparticles (NPs) stabilized by various amines (hexadecylamine, dodecylamine, and octylamine) in C₇D₈ demonstrated that the surface of this apparently simple system was very complex. Using different NMR spectroscopic techniques (¹H, PGSE‐NMR, diffusion‐filtered ¹H NMR, NOESY, ROESY), we observed at least three different modes of interaction of the amines at the surface of the NPs, in thermodynamic equilibrium with the free amines, the relative populations of which varied with their concentration. The first mode corresponded to a strong interaction between a small amount of amine and the ZnO NPs (k_desorp≈13 s^?1). The second mode corresponded to a weak interaction between the amines and the surface of the ZnO NPs (k_off(2)≈50–60 s^?1). The third, and weakest, mode of interaction corresponded to the formation of a second ligand shell by the amine around the NPs that was held together through van der Waals interactions (k_off(1)≈25×10⁵ s^?1). The second and third modes were in fast exchange on the NMR timescales with the free amines. The strongly interacting amines at the NPs surface (first mode) were in slow exchange with the other modes. A complex hydrogen‐bonding network at the NPs surface was also observed, which did not only involve the coordinated amine but also THF and water molecules that remained from the synthesis.     

SEAL by NMR: Glyco‐Based Selenium‐Labeled Affinity Ligands Detected by NMR Spectroscopy

We report a method for the screening of interactions between proteins and selenium‐labeled carbohydrate ligands. SEAL by NMR is demonstrated with selenoglycosides binding to lectins where the selenium nucleus serves as an NMR‐active handle and reports on binding through ⁷⁷Se NMR spectroscopy. In terms of overall sensitivity, this nucleus is comparable to ¹³C NMR, while the NMR spectral width is ten times larger, yielding little overlap in ⁷⁷Se NMR spectroscopy, even for similar compounds. The studied ligands are singly selenated bioisosteres of methyl glycosides for which straightforward preparation methods are at hand and libraries can readily be generated. The strength of the approach lies in its simplicity, sensitivity to binding events, the tolerance to additives and the possibility of having several ligands in the assay. This study extends the increasing potential of selenium in structure biology and medicinal chemistry. We anticipate that SEAL by NMR will be a beneficial tool for the development of selenium‐based bioactive compounds, such as glycomimetic drug candidates.     

A Simple NMR‐Based Method for Studying the Spatial Distribution of Linkers within Mixed‐Linker Metal–Organic Frameworks

The spatial distribution of different linkers within mixed‐linker metal–organic frameworks crucially influences the properties of such materials. A simple and robust approach based on ¹H spin‐diffusion magic‐angle‐spinning nuclear magnetic resonance measurements and modeling of spin‐diffusion curves is presented; this approach facilitates the distinction between homogeneous and clustered distributions. The performance of the approach is demonstrated with an example of an aluminum‐based metal–organic material DUT‐5, which has framework consisting of biphenyl and bipyridyl dicarboxylic linkers. The distribution is shown to be homogeneous in this material. The approach could be applied to studying other spatially disordered crystalline materials.     

Drug Screening in Human Cells by NMR Spectroscopy Allows the Early Assessment of Drug Potency

Structure‐based drug development is often hampered by the lack of in vivo activity of promising compounds screened in vitro, due to low membrane permeability or poor intracellular binding selectivity. Herein, we show that ligand screening can be performed in living human cells by “intracellular protein‐observed” NMR spectroscopy, without requiring enzymatic activity measurements or other cellular assays. Quantitative binding information is obtained by fast, inexpensive ¹H NMR experiments, providing intracellular dose‐ and time‐dependent ligand binding curves, from which kinetic and thermodynamic parameters linked to cell permeability and binding affinity and selectivity are obtained. The approach was applied to carbonic anhydrase and, in principle, can be extended to any NMR‐observable intracellular target. The results obtained are directly related to the potency of candidate drugs, that is, the required dose. The application of this approach at an early stage of the drug design pipeline could greatly increase the low success rate of modern drug development.     

Structure‐Based Approach To Improve a Small‐Molecule Inhibitor by the Use of a Competitive Peptide Ligand

Structural information about the target–compound complex is invaluable in the early stage of drug discovery. In particular, it is important to know into which part of the initial compound additional interaction sites could be introduced to improve its affinity. Herein, we demonstrate that the affinity of a small‐molecule inhibitor for its target protein could be successfully improved by the constructive introduction of the interaction mode of a competitive peptide. The strategy involved the discrimination of overlapping and non‐overlapping peptide–compound pharmacophores by the use of a ligand‐based NMR spectroscopic approach, INPHARMA. The obtained results enabled the design of a new compound with improved affinity for the platelet receptor glycoprotein VI (GPVI). The approach proposed herein efficiently combines the advantages of compounds and peptides for the development of higher‐affinity druglike ligands.     

PI by NMR: Probing CH–π Interactions in Protein–Ligand Complexes by NMR Spectroscopy

While CH–π interactions with target proteins are crucial determinants for the affinity of arguably every drug molecule, no method exists to directly measure the strength of individual CH–π interactions in drug–protein complexes. Herein, we present a fast and reliable methodology called PI (π interactions) by NMR, which can differentiate the strength of protein–ligand CH–π interactions in solution. By combining selective amino‐acid side‐chain labeling with ¹H‐¹³C NMR, we are able to identify specific protein protons of side‐chains engaged in CH–π interactions with aromatic ring systems of a ligand, based solely on ¹H chemical‐shift values of the interacting protein aromatic ring protons. The information encoded in the chemical shifts induced by such interactions serves as a proxy for the strength of each individual CH–π interaction. PI by NMR changes the paradigm by which chemists can optimize the potency of drug candidates: direct determination of individual π interactions rather than averaged measures of all interactions.     

Post‐Synthetic Ligand Exchange in Zirconium‐Based Metal–Organic Frameworks: Beware of The Defects!

Post‐synthetic ligand exchange in the prototypical zirconium‐based metal–organic framework (MOF) UiO‐66 was investigated by in situ solution ¹H NMR spectroscopy. Samples of UiO‐66 having different degrees of defectivity were exchanged using solutions of several terephthalic acid analogues in a range of conditions. Linker exchange only occurred in defect‐free UiO‐66, whereas monocarboxylates grafted at defect sites were found to be preferentially exchanged with respect to terephthalic acid over the whole range of conditions investigated. A 1:1 exchange ratio between the terephthalic acid analogue and modulator was observed, providing evidence that the defects had missing‐cluster nature. Ex situ characterisation of the MOF powders after exchange corroborated these findings and showed that the physical‐chemical properties of the MOF depend on whether the functionalisation occurs at defective sites or on the framework.