Computational prediction of complex cationic rearrangement outcomes

Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.

Modified glucose as a sensor to track the metabolism of individual living endothelial cells - Observation of the 1602 cm−1 band called “Raman spectroscopic signature of life”

A relatively new approach to subcellular research is Raman microscopy with the application of sensors called Raman probes. This paper describes the use of the sensitive and specific Raman probe, 3-O-propargyl-d-glucose (3-OPG), to track metabolic changes in endothelial cells (ECs). ECs play a significant role in a healthy and dysfunctional state, the latter is correlated with a range of lifestyle diseases, particularly with cardiovascular disorders. The metabolism and glucose uptake may reflect the physiopathological conditions and cell activity correlated with energy utilization. To study metabolic changes at the subcellular level the glucose analogue, 3-OPG was used, which shows a characteristic and intense Raman band at 2124 cm^-1.3-OPG was applied as a sensor to track both, its accumulation in live and fixed ECs and then metabolism in normal and inflamed ECs, by employing two spectroscopic techniques, i.e. spontaneous and stimulated Raman scattering microscopies. The results indicate that 3-OPG is a sensitive sensor to follow glucose metabolism, manifested by the Raman band of 1602 cm^-1. The 1602 cm^-1 band has been called the "Raman spectroscopic signature of life" in the cell literature, and here we demonstrate that it is attributed to glucose metabolites. Additionally, we have shown that glucose metabolism and its uptake are slowed down in the cellular inflammation. We showed that Raman spectroscopy can be classified as metabolomics, and its uniqueness lies in the fact that it allows the analysis of the processes of a single living cell. Gaining further knowledge on metabolic changes in the endothelium, especially in pathological conditions, may help in identifying markers of cellular dysfunction, and more broadly in cell phenotyping, better understanding of the mechanism of disease development and searching for new treatments.

Changes in the mitochondrial membrane potential in endothelial cells can be detected by Raman microscopy

The role of mitochondria goes beyond their capacity to create molecular fuel and includes e.g. the production of reactive oxygen species and the regulation of cell death. In endothelial cells, mitochondria have a significant impact on cellular function under both healthy and pathological conditions. Endothelial dysfunction contributes to the development of various lifestyle diseases and the key players in their pathogenesis are among others vascular inflammation and oxidative stress. The latter is very closely related to mitochondrial dysfunction; however, it is not straightforward. First, because mitochondria are small cellular structures, and second, it requires a sensitive method to follow the subtle biochemical changes. For this purpose, Raman microscopy (RM) was used here, which is considered a high-resolution method and can be applied in situ, usually as a non-labeled technique. In this work, we show that RM can not only locate mitochondria in the cell but also track their functional changes. Moreover, we test if labeling cells with Raman probes (Rp) can improve the specificity and sensitivity of RM (compared to conventional labeled techniques such as fluorescence, and the non-labeled Raman technique). MitoBADY Rp was used to detect changes in mitochondrial membrane potential as an indicator of mitochondrial activity, e.g. hyperpolarization or distortion of the proton gradient in the intermembrane space (depolarization). Thus, we show and compare RM, in the form of a label and non-labeled, to such a subtle cellular analysis.

EdU sensing: The Raman way of following endothelial cell proliferation in vitro and ex vivo

Endothelial cells line the lumen of all vessels in the body and maintain vascular homeostasis. In particular, endothelial cell regeneration in response to insult sustain functional endothelial layer. EdU (5-ethynyl-2'-deoxyuridine) is an alkyne-tagged proliferation probe that incorporates into newly synthesized DNA and is used for fluorescence imaging of cell proliferation with the use of "click chemistry" reaction with a fluorescent azide. Here, we utilized EdU as a click-free Raman probe for tracking endothelial cell proliferation. Raman imaging of EdU was performed in live endothelial cells, showing an advantage over fluorescence imaging of EdU, as this technique did not require sample fixation and permeabilization. To validate Raman-based imaging of EdU to study endothelial cell proliferation, we showed that when endothelial cells were treated with cycloheximide or doxorubicin to impair the proliferation of endothelial cells, the Raman-based signal of EdU was diminished. Furthermore, endothelial cells proliferation detected using EdU-labelled Raman imaging was compared with fluorescence imaging. Finally, the method of Raman-based EdU imaging was used in the isolated murine aorta ex vivo. Altogether, our results show that Raman-based imaging of EdU provides a novel alternative for fluorescence-based assay to assess endothelial proliferation and regeneration.

Propargylation of CoQ0 through the Redox Chain Reaction

An efficient catalytic propargylation of CoQ0 is described by employing the cooperative effect of Sc(OTf)₃ and Hantzsch ester. It is suggested to work through the redox chain reaction, which involves hydroquinone and dimeric propargylic moiety intermediates. A broad range of propargylic alcohols can be converted into the appropriate derivatives of CoQ0 containing triple bonds in good to excellent yields. The mechanism of the given transformation is also discussed.

Multiplex Raman imaging of organelles in endothelial cells

Raman imaging using molecular reporters is a relatively new approach in subcellular investigations. It enables the visualization of organelles in cells with better selectivity and sensitivity compared to the label-free approach. Essentially Raman reporters possess in their structure an alkyne molecular group that can be selectively identified in the spectral region silent for biomolecules, hence facilitate the localization of individual organelles. The aim of this work is to visualize the main cell organelles in endothelial cells (HMEC-1) using established reporters (EdU and MitoBADY), but also to test a new one, namely falcarinol, which exhibits lipophilic properties. Moreover, we tested the possibility to use Raman reporters as a probe to detect changes in distribution of certain organelles after induced endothelial dysfunction (ED) in in vitro models. In both cases, induced ED is characterized by the formation of lipid droplets in the cells, which is why a good tool for the detection of lipid-rich organelles is so important in these studies. Two-dimensional Raman images were obtained, visualizing the distribution of selected organic compounds in the cell, such as proteins, lipids, and nucleic acids. Additionally, the distribution of EdU, MitoBADY and falcarinol in endothelial cells (ECs) was determined. Moreover, we highlight some drawback of established Raman reporter and the need for testing them in various physiological state of the cell.

Nicotinamide N-methyltransferase in endothelium protects against oxidant stress-induced endothelial injury

Nicotinamide N-methyltransferase (NNMT, EC 2.1.1.1.) plays an important role in the growth of many different tumours and is also involved in various non-neoplastic disorders. However, the presence and role of NNMT in the endothelium has yet to be specifically explored. Here, we characterized the functional activity of NNMT in the endothelium and tested whether NNMT regulates endothelial cell viability. NNMT in endothelial cells (HAEC, HMEC-1 and EA.hy926) was inhibited using two approaches: pharmacological inhibition of the enzyme by NNMT inhibitors (5-amino-1-methylquinoline - 5MQ and 6-methoxynicotinamide - JBSF-88) or by shRNA-mediated silencing. Functional inhibition of NNMT was confirmed by LC/MS/MS-based analysis of impaired MNA production. The effects of NNMT inhibition on cellular viability were analyzed in both the absence and presence of menadione. Our results revealed that all studied endothelial lines express relatively high levels of functionally active NNMT compared with cancer cells (MDA-MB-231). Although the aldehyde oxidase 1 enzyme was also expressed in the endothelium, the further metabolites of N1-methylnicotinamide (N1-methyl-2-pyridone-5-carboxamide and N1-methyl-4-pyridone-3-carboxamide) generated by this enzyme were not detected, suggesting that endothelial NNMT-derived MNA was not subsequently metabolized in the endothelium by aldehyde oxidase 1. Menadione induced a concentration-dependent decrease in endothelial viability as evidenced by a decrease in cell number that was associated with the upregulation of NNMT and SIRT1 expression in the nucleus in viable cells. The suppression of the NNMT activity either by NNMT inhibitors or shRNA-based silencing significantly decreased the endothelial cell viability in response to menadione. Furthermore, NNMT inhibition resulted in nuclear SIRT1 expression downregulation and upregulation of the phosphorylated form of SIRT1 on Ser47. In conclusion, our results suggest that the endothelial nuclear NNMT/SIRT1 pathway exerts a cytoprotective role that safeguards endothelial cell viability under oxidant stress insult.

Comparative Assessment of the New PDE7 Inhibitor - GRMS-55 and Lisofylline in Animal Models of Immune-Related Disorders: A PK/PD Modeling Approach

Purpose

This study aimed to assess the activity of two phosphodiesterase (PDE) inhibitors, namely GRMS-55 and racemic lisofylline ((±)-LSF)) in vitro and in animal models of immune-mediated disorders.

Methods

Inhibition of human recombinant (hr)PDEs and TNF-alpha release from LPS-stimulated whole rat blood by the studied compounds were assessed in vitro. LPS-induced endotoxemia, concanavalin A (ConA)-induced hepatitis, and collagen-induced arthritis (CIA) animal models were used for in vivo evaluation. The potency of the investigated compounds was evaluated using PK/PD and PK/PD/disease progression modeling.

Results

GRMS-55 is a potent hrPDE7A and hrPDE1B inhibitor, while (±)-LSF most strongly inhibits hrPDE3A and hrPDE4B. GRMS-55 decreased TNF-alpha levels in vivo and CIA progression with IC₅₀ of 1.06 and 0.26 mg/L, while (±)-LSF with IC₅₀ of 5.80 and 1.06 mg/L, respectively. Moreover, GRMS-55 significantly ameliorated symptoms of ConA-induced hepatitis.

Conclusions

PDE4B but not PDE4D inhibition appears to be mainly engaged in anti-inflammatory activity of the studied compounds. GRMS-55 and (±)-LSF seem to be promising candidates for future studies on the treatment of immune-related diseases. The developed PK/PD models may be used to assess the anti-inflammatory and anti-arthritic potency of new compounds for the treatment of rheumatoid arthritis and other inflammatory disorders.

Electronic supplementary material

The online version of this article (10.1007/s11095-019-2727-z) contains supplementary material, which is available to authorized users.

Chiral Amplification in Nature: Studying Cell-Extracted Chiral Carotenoid Microcrystals via the Resonance Raman Optical Activity of Model Systems

Carotenoid microcrystals, extracted from cells of carrot roots and consisting of 95 % of achiral β-carotene, exhibit a very intense chiroptical (ECD and ROA) signal. The preferential chirality of crystalline aggregates that consist mostly of achiral building blocks is a newly observed phenomenon in nature, and may be related to asymmetric information transfer from the chiral seeds (small amount of α-carotene or lutein) present in carrot cells. To confirm this hypothesis, we synthesized several model aggregates from various achiral and chiral carotenoids. Because of the sergeant-and-soldier behavior, a small number of chiral sergeants (α-carotene or astaxanthin) force the achiral soldier molecules (β- or 11,11'-[D₂ ]-β-carotene) to jointly form supramolecular assemblies of induced chirality. The chiral amplification observed in these model systems confirmed that chiral microcrystals appearing in nature might consist predominantly of achiral building blocks and their supramolecular chirality might result from the co-crystallization of chiral and achiral analogues.

Asymmetric total synthesis of (+)-asenapine

Asymmetric total synthesis of (+)-asenapine, an atypical antipsychotic drug, used for treating schizophrenia and acute mania associated with bipolar disorder, is reported. The key steps are the organocatalytic Michael addition of aldehydes to trans-nitroalkenes and subsequent reductive cyclization.

Influence of inflammatory disorders on pharmacokinetics of lisofylline in rats: implications for studies in humans

1. Despite the number of favourable properties of lisofylline (LSF), clinical trials on this compound have not yielded the expected results yet. 2. The aims of this study were to evaluate the pharmacokinetics of LSF enantiomers in rats following intravenous, oral and subcutaneous administration of (±)-LSF and to assess the influence of experimental inflammatory disorders, such as multiple organ dysfunction syndrome and severe sepsis on LSF pharmacokinetics. 3. In addition, based on the results obtained an attempt was made to elucidate the possible reasons for the failure of LSF therapy in clinical trials carried out in patients with severe inflammatory disorders. 4. A subcutaneous route of (±)-LSF administration to rats is more favourable than an oral one due to a high bioavailability and a fast absorption of both LSF enantiomers. Pharmacokinetics of LSF in rats is significantly influenced by inflammatory diseases. Too low LSF serum levels might have been one of the reasons for clinical trial failures. A long-term i.v. infusion of LSF seems to be more effective compared to short-term multiple infusions that were used in clinical trials, as it may provide concentrations above IC₅₀ for inhibition of both TNF-alpha release and cAMP degradation in serum for a longer period of time.

Intramolecular Tandem Seleno-Michael/Aldol Reaction: A Simple Route to Hydroxy Cyclo-1-ene-1-carboxylate Esters

Intramolecular tandem seleno-Michael/aldol reaction followed by an oxidation-elimination process can be an efficient tool for the construction of hydroxy cyclo-1-ene-1-carboxylate esters from oxo-α,β-unsaturated esters. Generation of lithium selenolate from elemental selenium and n-BuLi provides a simple and efficient one-pot access to cyclic endo-Morita-Baylis-Hillman adducts.

Total synthesis of pipecolic acid and 1-C-alkyl 1,5-iminopentitol derivatives by way of stereoselective aldol reactions from (S)-isoserinal

A short synthesis of iminosugars and pipecolic acid derivatives has been realized through aldol addition of a pyruvate, a range of ketones and (S)-isoserinal, followed by catalytic reductive intramolecular amination. The stereoselective aldol reaction was achieved successfully by using tertiary amines or di-zinc aldol catalysts, thus constituting two parallel routes to optically pure products with good yields and high diastereoselectivities. These carbohydrate analogues may be the inhibitors of potent glycosidases and glycosyltransferases.

Iron-Catalyzed Asymmetric Nitro-Mannich Reaction

The first enantioselective addition of nitroalkanes to imines (nitro-Mannich reaction), mediated by an iron(II) catalyst assembled by a hindered hydroxyethyl-pybox ligand, is described. This valuable carbon-carbon bond-forming reaction proceeds smoothly at room temperature to afford enantioenriched β-nitro amines in good yields and high enantioselectivity, up to 98% with unprecedentedly low iron catalyst loading (5 mol %).

Self-Enhancement of Rotating Magnetocaloric Effect in Anisotropic Two-Dimensional (2D) Cyanido-Bridged MnII-NbIV Molecular Ferrimagnet

The rotating magnetocaloric effect (RMCE) is a new issue in the field of magnetic refrigeration. We have explored this subject on the two-dimensional (2D) enantiopure {[Mn^II(R-mpm)₂]₂[Nb^IV(CN)₈]}·4H₂O (where mpm = α-methyl-2-pyridinemethanol) coordination ferrimagnet. In this study, the magnetic and magnetocaloric properties of single crystals were investigated along the bc//H easy plane and the a*//H hard axis. The observed small easy plane anisotropy is due to the dipole-dipole interactions. For fields higher than 0.5 T, no significant difference in the magnetocaloric effect between both geometries was noticed. The maximal magnetic entropy change for conventional effect was observed at 32 K and the magnetic field change μ₀ΔH = 5.0 T attaining the value of ∼5 J mol^-1 K^-1. The obtained maximal value of -ΔS_m is comparable to previously reported results for polycrystalline octacyanidoniobate-based bimetallic coordination polymers. A substantial anisotropy of magnetocaloric effect between the easy plane and hard axis appears in low fields. This includes the presence of inverse magnetocaloric effect only for the a*//H direction. The difference between both geometries was used to study the rotating magnetocaloric effect. We show that the inverse part of magnetocaloric effect can be used to enhance the rotating magnetic entropy change up to 51%. This finding is of key importance for searching efficient materials for RMCE.

Synthesis of l-Pyranosides by Hydroboration of Hex-5-enopyranosides Revisited

Extensive study of the diastereoselective synthesis of l-pyranosides utilizing hydroboration of substituted exo-glucals (5-enopyranosides) obtained from d-sugars is presented. On the basis of this study we present the empirical rules describing the reaction stereoselectivity and the correlation between the yield of the l-ido product and the size of protecting groups used. Application of these guidelines revealed that the hydroboration of methyl 2,3-O-methyl-6-deoxy-α-d-xylo-hex-5-enopyranoside resulted in exclusive formation of l-ido product with high yield. This method can be successfully applied to the synthesis of l-iduronic acid being an essential component of anticoagulant drugs with diastereoselectivity superior to previously published protocols.

Synthesis of 2-Keto-d- and l-gluconic Acid via Stereoselective Direct Aldol Reactions

Stereoselective direct aldol reaction between optically pure d- or l-glyceraldehyde and hydroxyacetylfuran is demonstrated as an efficient and straightforward methodology for the synthesis of six-carbon atom d- and l-arabino-hex-2-ulosonic acids. syn-Selective aldol reactions realized by using either tertiary amines or a dizinc aldol catalyst constitute two parallel routes to the de novo synthesis of orthogonally protected biologically relevant 2-keto-d- and l-gluconic acids.

Enantioselective Hydrosilylation of Imines Catalyzed by Chiral Zinc Acetate Complexes

A series of zinc acetate complexes with optically pure diphenylethanediamine (DPEDA)-derived ligands have been employed as enantioselective catalyst for the hydrosilylation of various imines. High control of stereoselectivity (up to 97% ee) and excellent yields (up to 96%) were gained for a broad range of N-phosphinoylimines by using (R,R)-N,N'-dibenzyl-1,2-diphenylethane-1,2-diamine. This is the first successful application of an air-stable and environmentally friendly chiral Zn(OAc)2 complex instead of the previously used harmful diethylzinc in the asymmetric reduction of the C═N double bond.

Organocatalytic Synthesis of Higher-Carbon Sugars: Efficient Protocol for the Synthesis of Natural Sedoheptulose and d-Glycero-l-galacto-oct-2-ulose

Herein we report a short and efficient protocol for the synthesis of naturally occurring higher-carbon sugars-sedoheptulose (d-altro-hept-2-ulose) and d-glycero-l-galacto-oct-2-ulose-from readily available sugar aldehydes and dihydroxyacetone (DHA). The key step includes a diastereoselective organocatalytic syn-selective aldol reaction of DHA with d-erythrose and d-xylose, respectively. The methodology presented can be expanded to the synthesis of various higher sugars by means of syn-selective carbon-carbon-bond-forming aldol reactions promoted by primary-based organocatalysts. For example, this methodology provided useful access to d-glycero-d-galacto-oct-2-ulose and 1-deoxy-d-glycero-d-galacto-oct-2-ulose from d-arabinose in high yield (85 and 74 %, respectively) and high stereoselectivity (99:1).

Amine-catalyzed direct aldol reactions of hydroxy- and dihydroxyacetone: biomimetic synthesis of carbohydrates

This article presents comprehensive studies on the application of primary, secondary, and tertiary amines as efficient organocatalysts for the de novo synthesis of ketoses and deoxyketoses. Mimicking the actions of aldolase enzymes, the synthesis of selected carbohydrates was accomplished in aqueous media by using proline- and serine-based organocatalysts. The presented methodology also provides direct access to unnatural L-carbohydrates from the (S)-glyceraldehyde precursor. Determination of the absolute configuration of all obtained sugars was feasible using a methodology consisting of concerted ECD and VCD spectroscopy.