The benefits of Cu Kß radiation for the single-crystal X-ray structure determination of crystalline sponges.

The crystalline sponge method facilitates the X-ray structure determination of samples that do not crystallize or are too sparsely available to afford viable crystallization. By including these materials in a metal-organic framework, the structure of the guest molecules can be determined. Some of the inherent difficulties of this method are discussed and the use of Cu Kß radiation is presented as a simple and effective means to improve the quality of the diffraction data that can be obtained from a sponge crystal.

Metabolic Profiling of S-praziquantel: Structure Elucidation Using the Crystalline Sponge Method in Combination with Mass Spectrometry and Nuclear Magnetic Resonance.

Praziquantel (PZQ) is the drug of choice for treatment of the neglected tropical disease schistosomiasis. Although the drug has been extensively used over several decades and its metabolism well studied (several oxidative metabolites are known from literature), the knowledge of the complete structure of some of its metabolites remains elusive. Conventional techniques, such as nuclear magnetic resonance or liquid chromatography mass spectrometry were used in the past to investigate phase I and phase II metabolites of PZQ. These techniques are either limited to provide the complete molecular structure (liquid chromatography mass spectrometry) or require large amount of sample material (NMR), which are not always available when in vitro systems are used for investigation of the metabolites. In this study, we describe new structures of S-PZQ metabolites generated in vitro from human liver microsomes using the crystalline sponge method. After chromatographic separation and purification of the oxidative metabolites, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry analysis was conducted to narrow down the position of oxidation to a certain part of the molecule. To determine the exact position of hydroxylation, singe-crystal X-ray diffraction analysis of the crystalline sponges and absorbed analyte was used to identify the structure of S-PZQ and its metabolites. The crystalline sponge method allowed for complete structure elucidation of the known metabolites S-trans-4'-hydroxy-PZQ (M1), S-cis-4'-hydroxy-PZQ (M2) and S-/R-11b-hydroxy-PZQ (M6) as well as the unknown metabolites S-9-hydroxy-PZQ (M3) and S-7-hydroxy-S-PZQ (M4). For comparison of structural elucidation techniques, one metabolite (M3) was additionally analyzed using NMR. SIGNIFICANCE STATEMENT: The information content of the metabolic pathway of praziquantel is still limited. The crystalline sponge method allowed the complete structural elucidation of three known and two unknown metabolites of S-praziquantel, using only trace amounts of analyte material, as demonstrated in this study.

Crystalline sponge affinity screening: A fast tool for soaking condition optimization without the need of X-ray diffraction analysis.

Structural elucidation of small molecules only available in low quantity (nanogram) is one of the big advantages of the crystalline sponge method. The optimization of various soaking parameters is crucial for effective analyte absorption and repetitive positioning in the pores of the crystal. Time-consuming X-ray diffraction measurements are necessary for data collection and confirmation of successful guest inclusion. In this work, we report a screening method to select optimal soaking conditions without the need of single-crystal X-ray diffraction analysis for individual compounds and mixtures. 14 substances were chosen as test compounds. Parallel guest soaking of individual compounds and mixtures was conducted using various soaking conditions. After evaporation of solvent, excessive material was removed, and guest molecules released through dissolution of the framework. Liquid chromatography-tandem mass spectrometry allowed the estimation of analyte trapped in the pores and the selection of optimal soaking condition dependent on the highest amount of analyte to crystal size (affinity factor). The tool allowed subsequent crystallographic analysis of ten compounds with minimal experiment time. Additionally, a study to examine the lower limit of detection of the crystalline sponge method was conducted. Determination of two target analytes was possible using only 5 ng of sample. Our study shows the potential of an affinity screening to prioritize soaking parameters by estimation of the guest concentration in a single crystal for one or multiple target compounds within a short period of time.

Crystalline Sponges as a Sensitive and Fast Method for Metabolite Identification: Application to Gemfibrozil and its Phase I and II Metabolites.

Understanding the metabolism of new drug candidates is important during drug discovery and development, as circulating metabolites may contribute to efficacy or cause safety issues. In the early phase of drug discovery, human in vitro systems are used to investigate human relevant metabolism. Though conventional techniques are limited in their ability to provide complete molecular structures of metabolites (liquid chromatography mass spectrometry) or require a larger amount of material not available from in vitro incubation (nuclear magnetic resonance), we here report for the first time the use of the crystalline sponge method to identify phase I and phase II metabolites generated from in vitro liver microsomes or S9 fractions. Gemfibrozil was used as a test compound. Metabolites generated from incubation with microsomes or S9 fractions, were fractionated using online fraction collection. After chromatographic purification and fractionation of the generated metabolites, single crystal X-ray diffraction of crystalline sponges was used to identify the structure of gemfibrozil metabolites. This technique allowed for complete structure elucidation of 5'-CH2OH gemfibrozil (M1), 4'-OH gemfibrozil (M2), 5'-COOH gemfibrozil (M3), and the acyl glucuronide of gemfibrozil, 1-O-ß-glucuronide (M4), the first acyl glucuronide available in the Cambridge Crystallographic Data Centre. Our study shows that when optimal soaking is possible, crystalline sponges technology is a sensitive (nanogram amount) and fast (few days) method that can be applied early in drug discovery to identify the structure of pure metabolites from in vitro incubations. SIGNIFICANCE STATEMENT: Complete structure elucidation of human metabolites plays a critical role in early drug discovery. Low amounts of material (nanogram) are only available at this stage and insufficient for nuclear magnetic resonance analysis. The crystalline sponge method has the potential to close this gap, as demonstrated in this study.

Redox-Responsive Host-Guest Chemistry of a Flexible Cage with Naphthalene Walls.

"Naphthocage", a naphthalene-based organic cage, reveals very strong binding (up to 1010 M-1) to aromatic (di)cationic guests, i.e., the tetrathiafulvalene mono- and dication and methyl viologen. Intercalation of the guests between two naphthalene walls is mediated by C-H···O, C-H···π, and cation···π interactions. The guests can be switched into and out of the cage by redox processes with high binding selectivity. Oxidation of the flexible cage itself in the absence of a guest leads to a stable radical cation with the oxidized naphthalene intercalated between and stabilized by the other two. Encapsulated guest cations are released from the cavity upon cage oxidation, paving the way to future applications in redox-controlled guest release or novel stimuli-responsive materials.

Halogen Bonds in 2,5-Dihalopyridine-Copper(I) Halide Coordination Polymers.

Two series of 2,5-dihalopyridine-Cu(I)A (A = I, Br) complexes based on 2-X-5-iodopyridine and 2-X-5-bromopyridine (X = F, Cl, Br and I) are characterized by using single-crystal X-ray diffraction analysis to examine the nature of C2-X2···A-Cu and C5-X5···A-Cu halogen bonds. The reaction of the 2,5-dihalopyridines and Cu(I) salts allows the synthesis of eight 1-D coordination polymers and a discrete structure. The resulting Cu(I)-complexes are linked by C-X···A-Cu halogen bonds forming 3-D supramolecular networks. The C-X···A-Cu halogen bonds formed between halopyridine ligands and copper(I)-bound halide ions are stronger than C-X···X'-C interactions between two 2,5-dihalopyridine ligands. The C5-I5···I-Cu and C5-Br5···Br-Cu halogens bonds are shorter for C2-fluorine than C2-chlorine due to the greater electron-withdrawing power of fluorine. In 2,5-diiodopyridine-Cu(I)Br complex, the shorter C2-I2···Br-Cu [3.473(5) Å] distances are due to the combined polarization of C2-iodine by C2-I2···Cu interactions and para-electronic effects offered by the C5-iodine, whilst the long halogen bond contacts for C5-I5···Br-Cu [3.537(5) Å] are indicative that C2-iodine has a less para-electronic influence on the C5-iodine. In 2-fluoro-5-X-pyridine-Cu(I) complexes, the C2-fluorine is halogen bond passive, while the other C2-halogens in 2,5-dihalopyridine-Cu(I), including C2-chlorine, participate in halogen bonding interactions.

Spin Switching with Triazolate-Strapped Ferrous Porphyrins.

Fe(III) porphyrins bridged with 1,2,3-triazole ligands were synthesized. Upon deprotonation, the triazolate ion coordinates to the Fe(III) ion, forming an overall neutral high-spin Fe(III) porphyrin in which the triazolate serves both as an axial ligand and as the counterion. The second axial coordination site is activated for coordination and binds p-methoxypyridine, forming a six-coordinate low-spin complex. Upon addition of a phenylazopyridine as a photodissociable ligand, the spin state of the complex can be reversibly switched with ultraviolet and visible light. The system provides the basis for the development of switchable catalase- and peroxidase-type catalysts and molecular spin switches.

Asymmetric Synthesis of Spirocyclic ß-Lactams through Copper-Catalyzed Kinugasa/Michael Domino Reactions.

The first copper-catalyzed highly chemo-, regio-, diastereo-, and enantioselective Kinugasa/Michael domino reaction for the desymmetrization of prochiral cyclohexadienones is described. In the presence of a chiral copper catalyst, alkyne-tethered cyclohexadienones couple with nitrones to generate the chiral spirocyclic lactams with excellent stereoselectivity (up to 97 % ee, >20:1 dr). The new method provides direct access to versatile highly functionalized spirocyclic ß-lactams possessing four contiguous stereocenters, including one quaternary and one tetra-substituted stereocenter.

Asymmetric synthesis of functionalized tetrahydrofluorenones via an NHC-catalyzed homoenolate Michael addition.

The first example of an N-heterocyclic carbene-catalyzed asymmetric desymmetrization of enal-tethered cyclohexadienones via an intramolecular homoenolate Michael addition/esterification reaction is described. This new protocol offers a direct entry to various functionalized tetrahydrofluorenones with three contiguous stereocenters in high yields, good diastereoselectivities and excellent enantioselectivities.

Organocatalytic Oxa-Michael/Michael/Michael/Aldol Condensation Quadruple Domino Sequence: Asymmetric Synthesis of Tricyclic Chromanes.

An efficient and highly stereoselective one-pot, four-component synthesis of functionalized tricyclic chromanes has been achieved through an organocatalyzed quadruple domino reaction. The reaction sequence involves an oxa-Michael/Michael/Michael/aldol condensation between alcohols, 2 equiv of acrolein, and nitrochromenes to generate the pharmaceutically important tricyclic chromanes bearing three contiguous stereogenic centers including a chiral tetrasubstituted carbon center in good domino yields (30-70%) and excellent diastereo- and enantioselectivities (>20:1 dr and >99% ee).

Control of N-Heterocyclic Carbene Catalyzed Reactions of Enals: Asymmetric Synthesis of Oxindole-γ-Amino Acid Derivatives.

A strategy to control the switch between a non-cycloaddition reaction and a cycloaddition reaction of enals, using N-heterocyclic carbene (NHC) catalyisis, has been developed. The new scalable protocol leads to γ-amino-acid esters bearing a tetrasubstituted stereocenter in good yields and high stereoselectivities by homo-Mannich reactions of enals and isatin-derived ketimines. By simply changing the N-ketimine substituent to an ortho-hydroxy phenyl group, the corresponding spirocyclic oxindolo-γ-lactams are obtained.

N-Heterocyclic Carbene Catalyzed [3+2] Cycloaddition of Enals with Masked Cinnamates for the Asymmetric One-Pot Synthesis of Adipic Acid Derivatives.

A novel short entry to 3,4-disubstituted adipic acids has been developed by employing an asymmetric NHC-catalyzed [3+2] cycloaddition of enals with masked cinnammates in moderate to good yields and high stereoselectivities. The synthetic utility of the protocol was demonstrated by the basic conversion of the masked cyclopentanone intermediates to 3S,4S-disubstituted adipic acid precursors of pharmaceutically important gababutins.