Unraveling Complex Small‐Molecule Binding Mechanisms by Using Simple NMR Spectroscopy

Heteronuclear NMR spectroscopy provides a unique way to obtain site‐specific information about protein–ligand interactions. Usually, such studies rely on the availability of isotopically labeled proteins, thereby allowing both editing of the spectra and ligand signals to be filtered out. Herein, we report that the use of the methyl SOFAST correlation experiment enables the determination of site‐specific equilibrium binding constants by using unlabeled proteins. By using the binding of L ‐ and D ‐tryptophan to serum albumin as a test case, we determined very accurate dissociation constants for both the high‐ and low‐affinity sites present at the protein surface. The values of site‐specific dissociation constants were closer to those obtained by isothermal titration calorimetry than those obtained from ligand‐observed methods, such as saturation transfer difference. The possibility of measuring ligand binding to serum albumin at physiological concentrations with unlabeled proteins may open up new perspectives in the field of drug discovery.     

Microcrystal Electron Diffraction (MicroED) for Small‐Molecule Structure Determination

The development of new methods to analyze and determine molecular structures parallels the ability to accelerate synthetic research. For many decades, single‐crystal analysis by X‐ray diffraction (SXRD) has been the definitive tool for structural analysis at the atomic level; the drawback, however, is that a suitable single crystal of the analyte needs to be grown. The recent innovation of the crystalline sponge (CS) method allows the microanalysis of compounds simply soaked in a readily prepared CS crystal, thus circumventing the need to screen crystallization conditions while also using only a trace amount of the sample. In this context, electron diffraction for the structure determination of small molecules is discussed as potentially the next big development in this field.     

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.     

α‐ and β‐Glycosyl Sulfonium Ions: Generation and Reactivity

Low‐temperature electrochemical oxidation of thioglycosides gave glycosyl triflates from which glycosyl sulfonium ions were produced (see scheme). The latter were characterized by NMR spectroscopy and cold‐spray mass spectrometry as a mixture of α‐ and β‐isomers (45:55). The α‐glycosyl sulfonium ion exhibited higher reactivity than the β‐glycosyl sulfonium ion in the reaction with methanol, which gave a mixture of α‐ and β‐methyl glycosides (41:59).

     

Magnetically Induced Alignment of Natural Products for Stereochemical Structure Determination via NMR

Anisotropic NMR has gained increasing popularity to determine the structure and specifically the configuration of small, flexible, non‐crystallizable molecules. However, it suffers from the necessity to dissolve the analyte in special media such as liquid crystals or polymer gels. Generally, small degrees of alignment are also caused by an anisotropic magnetic susceptibility of the molecule, for example, induced by aromatic moieties. For this mechanism, the alignment can be predicted via density functional theory. Here we show that both residual dipolar couplings and residual chemical shift anisotropies can be acquired from natural products without special sample preparation using magnetically induced alignment. On the two examples of the novel natural product gymnochrome G and the alkaloid strychnine, these data, together with the predicted alignment, yield the correct configuration with high certainty.     

Synthesis and Stereochemical Revision of the C31–C67 Fragment of Amphidinol 3

Amphidinol 3 (AM3) is a marine natural product produced by the dinoflagellate Amphidinium klebsii. Although the absolute configuration of AM3 was determined in 1999 by extensive NMR analysis and degradation of the natural product, it was a daunting task because of the presence of numerous stereogenic centers on the acyclic carbon chain and the limited availability from natural sources. Thereafter, revisions of the absolute configurations at C2 and C51 were reported in 2008 and 2013, respectively. Reported herein is the revised absolute configuration of AM3: 32S, 33R, 34S, 35S, 36S, and 38S based on the chemical synthesis of partial structures corresponding to the C31–C67 fragment of AM3 in combination with degradation of the natural product. The revised structure is unique in that both antipodal tetrahydropyran counterparts exist on a single carbon chain. The structural revision of AM3 may affect proposed structures of congeners related to the amphidinols.     

A Zeolite‐Supported Molecular Ruthenium Complex with η6‐C6H6 Ligands: Chemistry Elucidated by Using Spectroscopy and Density Functional Theory

An essentially molecular ruthenium–benzene complex anchored at the aluminum sites of dealuminated zeolite Y was formed by treating a zeolite‐supported mononuclear ruthenium complex, [Ru(acac)(η²‐C₂H₄)₂]⁺ (acac=acetylacetonate, C₅H₇O₂^?), with ¹³C₆H₆ at 413 K. IR, ¹³C NMR, and extended X‐ray absorption fine structure (EXAFS) spectra of the sample reveal the replacement of two ethene ligands and one acac ligand in the original complex with one ¹³C₆H₆ ligand and the formation of adsorbed protonated acac (Hacac). The EXAFS results indicate that the supported [Ru(η⁶‐C₆H₆)]²⁺ incorporates an oxygen atom of the support to balance the charge, being bonded to the zeolite through three Ru? O bonds. The supported ruthenium–benzene complex is analogous to complexes with polyoxometalate ligands, consistent with the high structural uniformity of the zeolite‐supported species, which led to good agreement between the spectra and calculations at the density functional theory level. The calculations show that the interaction of the zeolite with the Hacac formed on treatment of the original complex with ¹³C₆H₆ drives the reaction to form the ruthenium–benzene complex.     

Small‐Molecule Recognition for Controlling Molecular Motion in Hydrogen‐Bond‐Assembled Rotaxanes

Di(acylamino)pyridines successfully template the formation of hydrogen‐bonded rotaxanes through five‐component clipping reactions. A solid‐state study showed the participation of the pyridine nitrogen atom in the stabilization of the mechanical bond between the thread and the benzylic amide macrocycle. The addition of external complementary binders to a series of interlocked bis(2,6‐di(acylamino)pyridines) promoted restraint of the back and forward ring motion. The original translation can be restored through a competitive recognition event by the addition of a preorganized bis(di(acylamino)pyridine) that forms stronger ADA–DAD complexes with the external binders.     

Metal‐Directed Self‐Assembly of a Polyoxometalate‐Based Molecular Triangle: Using Powerful Analytical Tools to Probe the Chemical Structure of Complex Supramolecular Assemblies

A polyoxometalate‐based molecular triangle has been synthesized through the metal‐driven self‐assembly of covalent organic/inorganic hybrid oxo‐clusters with remote pyridyl binding sites. The new metallomacrocycle was unambiguously characterized by using a combination of ¹H NMR spectroscopy, 2D diffusion NMR spectroscopy (DOSY), electrospray ionization travelling wave ion mobility mass spectrometry (ESI‐TWIM‐MS), small‐angle X‐ray scattering (SAXS) and molecular modelling. The collision cross‐sections obtained from TWIM‐MS and the hydrodynamic radii derived from DOSY are in good agreement with the geometry‐optimized structures obtained by using theoretical calculations. Furthermore, SAXS was successfully employed and proved to be a powerful technique for characterizing such large supramolecular assemblies.     

Stereochemical Studies on Ovatoxin‐a

Ovatoxin‐a is the main toxin produced by Ostreopsis ovata, a benthic dinoflagellate that has bloomed massively across the Mediterranean basin over the past years, inflicting both human and environmental suffering. Ovatoxin‐a has recently been isolated from cultures of O. ovata and structurally identified as an analogue of palytoxin: in comparison with palytoxin, ovatoxin‐a lacks three hydroxy groups at the 17‐, 44‐ and 64‐positions, but features an extra hydroxy functionality at the 42‐position. Herein we report on the NMR‐based elucidation of the stereochemistry of ovatoxin‐a, which includes 7 stereogenic double bonds and 62 asymmetric carbon atoms. Understanding the full stereochemistry of ovatoxin‐a is a step towards the elucidation of its mechanism of action on a molecular level.     

The prediction of the absolute stereochemistry of primary and secondary 1,2-diols by 1H NMR spectroscopy: principles and applications

The absolute configuration of 1,2-diols formed by a primary and a secondary (chiral) hydroxyl group can be deduced by comparison of the 1H NMR spectra of the corresponding (R)- and bis-(S)-MPA esters (MPA = methoxyphenylacetic acid). This method involves the use of the chemical shifts of substituents L1/L2 attached to the secondary (chiral) carbon, and of the hydrogen atom linked to the chiral center (C alpha-H) as diagnostic signals. Theoretical (AM1, HF, and B3 LYP calculations) and experimental data (dynamic and low-temperature NMR spectroscopy, studies on deuterated derivatives, constant coupling analysis, circular dichroism (CD) spectra, and NMR studies with a number of diols of known absolute configuration) prove that the signs of the delta delta(RS) obtained for those signals correlate with the absolute configuration of the diol. A graphical model for the reliable assignment of the absolute configuration of a 1,2-diol by comparison of the NMR spectra of its bis-(R)- and bis-(S)-MPA esters is presented.     

Matrix‐Free DNP‐Enhanced NMR Spectroscopy of Liposomes Using a Lipid‐Anchored Biradical

Magic‐angle spinning dynamic nuclear polarization (MAS‐DNP) has been proven to be a powerful technique to enhance the sensitivity of solid‐state NMR (SSNMR) in a wide range of systems. Here, we show that DNP can be used to polarize lipids using a lipid‐anchored polarizing agent. More specifically, we introduce a C16‐functionalized biradical, which allows localization of the polarizing agents in the lipid bilayer and DNP experiments to be performed in the absence of excess cryo‐protectant molecules (glycerol, dimethyl sulfoxide, etc.). This constitutes another original example of the matrix‐free DNP approach that we recently introduced.