Solution NMR Structure of a Ligand/Hybrid‐2‐G‐Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding

Telomeric G‐quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G‐quadruplex that adopts the biologically relevant hybrid‐2 conformation in a ligand‐bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G‐quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G‐quadruplex. The ligand is sandwiched between one terminal G‐tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G‐quadruplex structure as observed for other G‐quadruplexes in different conformations, invalidating simple docking approaches to ligand–G‐quadruplex structure determination.     

Ruthenium Lewis Acid‐Catalyzed Asymmetric Diels–Alder Reactions: Reverse‐Face Selectivity for α,β‐Unsaturated Aldehydes and Ketones

Acrolein, methacrolein, methyl vinyl ketone, ethyl vinyl ketone, 3‐methyl‐3‐en‐2‐one, and divinyl ketone were coordinated to a cationic cyclopentadienyl ruthenium(II) Lewis acid incorporating the electron‐poor bidentate BIPHOP–F ligand. Analysis by NOESY and ROESY NMR techniques allowed the determination of conformations of enals and enones present in solution in CD₂Cl₂. The results were compared to solid‐state structures and to the facial selectivities of catalytic asymmetric Diels–Alder reactions with cyclopentadiene. X‐Ray structures of four Ru‐enal and Ru‐enone complexes show the α,β‐unsaturated C=O compounds to adopt an anti‐s‐trans conformation. In solution, enals assume both anti‐s‐trans and anti‐s‐cis conformations. An additional conformation, syn‐s‐trans, is present in enone complexes. Enantioface selectivity in the cycloaddition reactions differs for enals and enones. Reaction products indicate enals to react exclusively in the anti‐s‐trans conformation, whereas with enones, the major product results from the syn‐s‐trans conformation. The alkene in s‐cis conformations, while present in solution, is shielded and cannot undergo cycloaddition. A syn‐s‐trans conformation is found in the solid state of the bulky 6,6‐dimethyl cyclohexanone‐Ru(II) complex. The X‐ray structure of divinyl ketone is unique in that the Ru(II) center binds the enone via a η² bond to one of the alkene moieties. In solution, coordination to Ru–C=O oxygen is adopted. A comparison of facial preference is also made to the corresponding indenyl Lewis acids.     

Quantitative Structural Constraints for Organic Powders at Natural Isotopic Abundance Using Dynamic Nuclear Polarization Solid‐State NMR Spectroscopy

A straightforward method is reported to quantitatively relate structural constraints based on ¹³C–¹³C double‐quantum build‐up curves obtained by dynamic nuclear polarization (DNP) solid‐state NMR to the crystal structure of organic powders at natural isotopic abundance. This method relies on the significant gain in NMR sensitivity provided by DNP (approximately 50‐fold, lowering the experimental time from a few years to a few days), and is sensitive to the molecular conformation and crystal packing of the studied powder sample (in this case theophylline). This method allows trial crystal structures to be rapidly and effectively discriminated, and paves the way to three‐dimensional structure elucidation of powders through combination with powder X‐ray diffraction, crystal‐structure prediction, and density functional theory computation of NMR chemical shifts.     

Solid‐State Structure of a Li/F Carbenoid: Pentafluoroethyllithium

Lithium carbenoids are versatile compounds for synthesis owing to their intriguing ambiphilic behavior. Although this class of compounds has been known for several years, few solid‐state structures exist because of their high reactivity and often low thermal stability. Using cryo X‐ray techniques, we were now able to elucidate the first solid‐state structure of a Li/F alkyl carbenoid, pentafluoroethyllithium (LiC₂F₅), finally yielding a prototype for investigating structure—reactivity relationships for this class of molecules. The compound forms a diethyl ether‐solvated dimer bridged by a rare C–F–Li link. Complementary NMR spectroscopy studies in solution show dynamic processes and indicate rapid exchange of starting material and product. Theoretical investigations help to understand the formation of the observed unusual structural motif.     

Conformational Analysis of the Cyclic Pentadepsipeptide Cyclo(Tro‐Aib‐Aib‐Aib‐Aib) in the Solid State and in Solution

The cyclic 16‐membered pentadepsipeptide cyclo(Tro‐Aib‐Aib‐Aib‐Aib) ( 1 ) was crystallized from MeOH/AcOEt/CH₂Cl₂, and its structure was established by X‐ray crystallography (Fig. 1). There are two symmetry‐independent molecules with different conformations in the asymmetric unit. Two intramolecular H‐bonds stabilize two β‐turns in each molecule. On the other hand, two of the four Aib residues are forced to assume a nonfavorable nonhelical conformation in each of the symmetry‐independent molecules (Table 1). The conformational study in CDCl₃ solution by NMR spectroscopy and molecular dynamics (MD) simulations indicate that the averaged structure (Fig. 3) is almost the same as in the solid state.     

Cyclic RGD peptidomimetics containing bifunctional diketopiperazine scaffolds as new potent integrin ligands

The synthesis of eight bifunctional diketopiperazine (DKP) scaffolds is described; these were formally derived from 2,3-diaminopropionic acid and aspartic acid (DKP-1-DKP-7) or glutamic acid (DKP-8) and feature an amine and a carboxylic acid functional group. The scaffolds differ in the configuration at the two stereocenters and the substitution at the diketopiperazinic nitrogen atoms. The bifunctional diketopiperazines were introduced into eight cyclic peptidomimetics containing the Arg-Gly-Asp (RGD) sequence. The resulting RGD peptidomimetics were screened for their ability to inhibit biotinylated vitronectin binding to the purified integrins α(v)β(3) and α(v)β(5), which are involved in tumor angiogenesis. Nanomolar IC(50) values were obtained for the RGD peptidomimetics derived from trans DKP scaffolds (DKP-2-DKP-8). Conformational studies of the cyclic RGD peptidomimetics by (1)H?NMR spectroscopy experiments (VT-NMR and NOESY spectroscopy) in aqueous solution and Monte Carlo/Stochastic Dynamics (MC/SD) simulations revealed that the highest affinity ligands display well-defined preferred conformations featuring intramolecular hydrogen-bonded turn motifs and an extended arrangement of the RGD sequence [Cβ(Arg)-Cβ(Asp) average distance ≥8.8??]. Docking studies were performed, starting from the representative conformations obtained from the MC/SD simulations and taking as a reference model the crystal structure of the extracellular segment of integrin α(v)β(3) complexed with the cyclic pentapeptide, Cilengitide. The highest affinity ligands produced top-ranked poses conserving all the important interactions of the X-ray complex.     

Synthesis,Coordination Chemistry and Bonding of Strong N‐Donor Ligands Incorporating the 1H‐Pyridin‐(2E)‐Ylidene (PYE) Motif

A range of N‐donor ligands based on the 1H‐pyridin‐(2E)‐ylidene (PYE) motif have been prepared, including achiral and chiral examples. The ligands incorporate one to three PYE groups that coordinate to a metal through the exocyclic nitrogen atom of each PYE moiety, and the resulting metal complexes have been characterised by methods including single‐crystal X‐ray diffraction and NMR spectroscopy to examine metal–ligand bonding and ligand dynamics. Upon coordination of a PYE ligand to a proton or metal‐complex fragment, the solid‐state structures, NMR spectroscopy and DFT studies indicate that charge redistribution occurs within the PYE heterocyclic ring to give a contribution from a pyridinium–amido‐type resonance structure. Additional IR spectroscopy and computational studies suggest that PYE ligands are strong donor ligands. NMR spectroscopy shows that for metal complexes there is restricted motion about the exocyclic C? N bond, which projects the heterocyclic N‐substituent in the vicinity of the metal atom causing restricted motion in chelating‐ligand derivatives. Solid‐state structures and DFT calculations also show significant steric congestion and secondary metal–ligand interactions between the metal and ligand C? H bonds.     

A Molecular Toolkit for the Functionalization of Titanium‐Based Biomaterials That Selectively Control Integrin‐Mediated Cell Adhesion

We present a click chemistry‐based molecular toolkit for the biofunctionalization of materials to selectively control integrin‐mediated cell adhesion. To this end, α5β1‐selective RGD peptidomimetics were covalently immobilized on Ti‐based materials, and the capacity to promote the selective binding of α5β1 was evaluated using a solid‐phase integrin binding assay. This functionalization strategy yielded surfaces with a nine‐fold increased affinity for α5β1, in comparison to control samples, and total selectivity against the binding of the closely related integrin αvβ3. Moreover, our methodology allowed the screening of several phosphonic acid containing anchoring units to find the best spacer–anchor moiety required for establishing an efficient binding to titanium and to promote selective integrin binding. The integrin subtype specificity of these biofunctionalized surfaces was further examined in vitro by inducing selective adhesion of genetically modified fibroblasts, which express exclusively the α5β1 integrin. The versatility of our molecular toolkit was proven by shifting the cellular specificity of the materials from α5β1‐ to αvβ3‐expressing fibroblasts by using an αvβ3‐selective peptidomimetic as coating molecule. The results shown here represent the first functionalization of Ti‐based materials with α5β1‐ or αvβ3‐selective peptidomimetics that allow an unprecedented control to discriminate between α5β1‐ and αvβ3‐mediated adhesions. The role of these two integrins in different biological events is still a matter of debate and is frequently discussed in literature. Thus, such bioactive titanium surfaces will be of great relevance for the study of integrin‐mediated cell adhesion and the development of new biomaterials targeting specific cell types.     

A Multifaceted Secondary Structure Mimic Based On Piperidine‐piperidinones

Minimalist secondary structure mimics are typically made to resemble one interface in a protein–protein interaction (PPI), and thus perturb it. We recently proposed suitable chemotypes can be matched with interface regions directly, without regard for secondary structures. Here we describe a modular synthesis of a new chemotype 1 , simulation of its solution‐state conformational ensemble, and correlation of that with ideal secondary structures and real interface regions in PPIs. Scaffold 1 presents amino acid side‐chains that are quite separated from each other, in orientations that closely resemble ideal sheet or helical structures, similar non‐ideal structures at PPI interfaces, and regions of other PPI interfaces where the mimic conformation does not resemble any secondary structure. 68 different PPIs where conformations of 1 matched well were identified. A new method is also presented to determine the relevance of a minimalist mimic crystal structure to its solution conformations. Thus dld ‐ 1 faf crystallized in a conformation that is estimated to be 0.91 kcal mol^?1 above the minimum energy solution state.     

Stable Peptides Instead of Stapled Peptides: Highly Potent αvβ6‐Selective Integrin Ligands

The αvβ6 integrin binds the RGD‐containing peptide of the foot and mouth disease virus with high selectivity. In this study, the long binding helix of this ligand was downsized to an enzymatically stable cyclic peptide endowed with sub‐nanomolar binding affinity toward the αvβ6 receptor and remarkable selectivity against other integrins. Computational studies were performed to disclose the molecular bases underlying the high binding affinity and receptor subtype selectivity of this peptide. Finally, the utility of the ligand for use in biomedical studies was also demonstrated here.     

Identification of a Conformational Equilibrium That Determines the Efficacy and Functional Selectivity of the μ‐Opioid Receptor

G‐protein‐coupled receptor (GPCR) ligands impart differing degrees of signaling in the G‐protein and arrestin pathways, in phenomena called “biased signaling”. However, the mechanism underlying the biased signaling of GPCRs is still unclear, although crystal structures of GPCRs bound to the G protein or arrestin are available. In this study, we observed the NMR signals from methionine residues of the μ‐opioid receptor (μOR) in the balanced‐ and biased‐ligand‐bound states. We found that the intracellular cavity of μOR exists in an equilibrium between closed and multiple open conformations with coupled conformational changes on the transmembrane helices 3, 5, 6, and 7, and that the population of each open conformation determines the G‐protein‐ and arrestin‐mediated signaling levels in each ligand‐bound state. These findings provide insight into the biased signaling of GPCRs and will be helpful for development of analgesics that stimulate μOR with reduced tolerance and dependence.     

Structure of the Ribosomal RNA Decoding Site Containing a Selenium‐Modified Responsive Fluorescent Ribonucleoside Probe

Comprehensive understanding of the structure–function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation‐sensitive fluorophore and an anomalous X‐ray diffraction label (5‐selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand‐induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.     

Synthesis,Crystal Structure,and Characterization of Two Novel Five‐coordinate Zinc(II) Complexes with the Tripod Ligand Tris(N‐methylbenzimidazol‐2‐yl‐methyl)amine and α,β‐unsaturated Carboxylates

Two novel five‐coordinate zinc(II) complexes with the tripod ligand tris(N‐methylbenzimidazol‐2‐ylmethyl)amine (Mentb) and two different α,β‐unsaturated carboxylates, with the composition [Zn(Mentb)(acrylate)] (ClO₄)·DMF·1.5CH₃OH ( 1 ) and [Zn(Mentb)(cinnamate)](ClO₄)·2DMF·0.5CH₃OH ( 2 ), were synthesized and characterized by means of elemental analyses, electrical conductivity measurements, IR, UV, and ¹H NMR spectra. The crystal structure of two complexes have been determined by a single‐crystal X‐ray diffraction method, and show that the Zn^II atom is bonded to a Mentb ligand and a α,β‐unsaturated carboxylate molecule through four N atoms and one O atom, resulting in a distorted trigonal‐bipyramidal coordination [τ( 1 ) = 0.853, τ( 2 ) = 0.855], with approximate C₃ symmetry.     

Powder X‐ray study of racemic (2RS,3RS)‐5‐amino‐3‐[4‐(3‐methoxyphenyl)piperazin‐1‐yl]‐1,2,3,4‐tetrahydronaphthalen‐2‐ol

The structure of the title benzovesamicol analogue, C₂₁H₂₇N₃O₂, an important compound for the diagnosis of Alzheimer's disease, has been determined by X‐ray powder diffraction. The title compound was firstly synthesized and characterized by spectroscopic methods (FT–IR, and ¹³C and ¹H NMR). The compound is a racemic mixture of enantiomers which crystallizes in the monoclinic system in a centrosymmetric space group (P2₁/c). Crystallography, in particular powder X‐ray diffraction, was pivotal in revealing that the enantio‐resolution did not succeed. The piperazine ring is in a chair conformation, while the cyclohexene ring assumes a half‐chair conformation. The crystal packing is dominated by intermolecular O—H...N hydrogen bonding which links molecules along the c direction.     

Conformations of the Nine‐Membered Ring in the B‐Nor‐5,10‐secosteroids. X‐Ray and NMR Analysis

The conformations of (Z)‐ and (E)‐5‐oxo‐B‐nor‐5,10‐secocholest‐1(10)‐en‐3β‐yl acetates ( 2 and 3 , resp.) were examined by a combination of X‐ray crystallographic analysis and NMR spectroscopy, with emphasis on the geometry of the cyclononenone moiety. The ¹H‐ and ¹³C‐NMR spectra showed that the unsaturated nine‐membered ring of (E)‐isomer 3 in C₆D₆ and (D₆)acetone solution exists in a sole conformation of type B ₁ , which is similar to its solid‐state conformation. The (Z)‐isomer 2 in C₆D₆, CDCl₃, and (D₆)acetone solution, however, exists in two conformational forms of different families, with different orientation of the carbonyl group, the predominant form (85%) corresponding to the conformation of type A ₁ and the minor (15%) to the conformation A ₂ present also in the crystalline state. In this solid‐state conformations of the nine‐membered ring of both compounds, the 19‐Me and 5‐oxo groups are ‘β’‐oriented. The NMR analysis suggests that the nine‐membered ring of 4 has a conformation of type C ₁ in CDCl₃ solution.     

Synthesis,Structural Characterisation and Stereochemical Investigation of Chiral Sulfur‐Functionalised N‐Heterocyclic Carbene Complexes of Palladium and Platinum

Palladium and platinum complexes containing a sulfur‐functionalised N‐heterocyclic carbene (S‐NHC) chelate ligand have been synthesised. The absolute conformations of these novel organometallic S‐NHC chelates were determined by X‐ray structural analyses and solution‐phase 2D ¹H–¹H ROESY NMR spectroscopy. The structural studies revealed that the phenyl substituents on the stereogenic carbon atoms invariably take up the axial positions on the Pd‐C‐S coordination plane to afford a skewed five‐membered ring structure. All of the chiral complexes are structurally rigid and stereochemically locked in a chiral ring conformation that is either (R_s,S,R)‐λ or (S_s,R,R)‐δ in both the solid state and solution.     

1,3‐Alternate Tetraamido‐Azacalix[4]arenes as Selective Anion Receptors

Six tetraaza[1.1.1.1]cyclophane derivatives bearing peripheral amide groups were prepared according to two distinct synthetic strategies that depend on the connection pattern between the aryl units. NMR experiments combined with the X‐ray structures of two tetraamide derivatives 4 b and 10 show that these cavitands adopt a 1,3‐alternate conformation both in solution and in the solid state. Consequently, the four amide groups of the aza[1.1.1.1]‐m,m,m,m‐cyclophane isomer 10 can contribute to the same recognition process towards neutral water molecules or anion guests. NMR experiments, mass spectrometry analyses and single‐crystal X‐ray structures confirm the anion‐binding ability of this receptor. Absorption spectrophotometric titrations in nonpolar solvents provided evidence for the selectivity of 10 to chloride anions in the halide series, with a corresponding association constant K_a reaching 2.5×10⁶ m ^?1.     

Spectroscopic characterization and molecular structure of 3,14‐dimethyl‐2,6,13,17‐tetraazapentacyclo[16.4.0.12,17.16,13.07,12]tetracosane

Constrained cyclam derivatives have been found to exhibit anti‐HIV effects. The strength of binding to the CXCR4 receptor correlates with anti‐HIV activity. The conformation of the macrocyclic compound is very important for co‐receptor recognition. Therefore, knowledge of the conformation and crystal packing of macrocycles has become important in developing new highly effective anti‐HIV drugs. Structural modifications of N‐functionalized polyaza macrocyclic compounds have been achieved using various methods. A new synthesis affording single crystals of the title tetraazapentacyclo[16.4.0.1^2,17.1^6,13.0^7,12]tetracosane macrocycle, C₂₂H₄₀N₄, is reported. Formaldehyde reacts readily at room temperature with the tetraazatricyclo[16.4.0.0^2,17]docosane precursor to yield a macropolycycle containing two five‐membered rings. Characterization by elemental, spectroscopic and single‐crystal X‐ray diffraction analyses shows that the asymmetric unit contains half of a centrosymmetric molecule. The molecular structure shows a trans conformation for the two methylene bridges owing to molecular symmetry. The crystal structure is stabilized by intramolecular C—H…N hydrogen bonds. NMR and IR spectroscopic properties support the methylene‐bridged macrocyclic structure.     

3‐Fluoro‐2,4‐dioxa‐7‐aza‐3‐phosphadecalin 3‐Oxides as Rigid Acetylcholine Mimetics: Conformational Analysis and Direct Evidence of the Anomeric Effect

Conformational analyses of the P(3)‐axially and P(3)‐equatorially F‐substituted (±)‐cis‐ and (±)‐trans‐2,4‐dioxa‐7‐aza‐3‐phosphadecalin 3‐oxides (3‐fluoro‐2,4‐dioxa‐7‐aza‐3‐phosphabicyclo[4.4.0]decane 3‐oxides) were performed. The results are based on independent studies in both solution and the solid state by ¹H‐ and ³¹P‐NMR experiments and computational and X‐ray crystallographic data. As expected, the axial epimers adopt neat double‐chair conformations in solution and in the crystal. Due to the anomeric effect of the electron withdrawing F‐substituent, the 2,4‐dioxa‐3‐phospha moiety in the equatorial epimers adopts a mixture of conformations in solution, mainly chair and twist‐boat; whereas a neat twist‐boat (trans‐isomer) and the unusual envelope conformation (cis‐isomer) were detected in the solid state. This is the first report of a straight visualization of these conformations and the impact of the anomeric effect in such systems.     

New azo‐azomethine‐based transition metal complexes: Synthesis,spectroscopy, solid‐state structure,density functional theory calculations and anticancer studies

A novel tetradentate azo‐Schiff base ligand (H₂L) was synthesized by 2:1 molar condensation of an azo‐aldehyde and ethylenediamine. Its mononuclear Cu(II), Ni(II), Co(II) and Zn(II) complexes were prepared and their structures were confirmed using elemental analysis, NMR, infrared and UV–visible spectroscopies and molar conductivity measurements. The results suggest that the metal ion is bonded to the tetradentate ligand through phenolic oxygens and imine nitrogens of the ligand. The solid‐state structures of the azo‐Schiff base ligand and its Cu(II) complex were determined using single‐crystal X‐ray diffraction studies. The azo‐Schiff base ligand lies on a crystallographic inversion centre and thus the asymmetric unit contains half of the molecule. X‐ray data revealed that keto–amine tautomer is favoured in the solid‐state structure of the ligand. In the structure of the Cu(II) complex, the Cu(II) ion is coordinated to two phenolate oxygen atoms and two imine nitrogen atoms of the azo‐Schiff base ligand with approximate square planar geometry. The anticancer activity of the synthesized complexes was investigated for human cancer cell line (MCF‐7) and cytotoxicity of the synthesized compounds was determined against mouse fibroblast cells (L929). The ligand and its complexes were found to show antitumor activity. The synthesized metal complexes were optimized at the B3LYP/LANL2DZ level and a new theoretical formula for MCF‐7 cells was also derived.