Automated radial synthesis of organic molecules.

Automated synthesis platforms accelerate and simplify the preparation of molecules by removing the physical barriers to organic synthesis. This provides unrestricted access to biopolymers and small molecules via reproducible and directly comparable chemical processes. Current automated multistep syntheses rely on either iterative1-4 or linear processes5-9, and require compromises in terms of versatility and the use of equipment. Here we report an approach towards the automated synthesis of small molecules, based on a series of continuous flow modules that are radially arranged around a central switching station. Using this approach, concise volumes can be exposed to any reaction conditions required for a desired transformation. Sequential, non-simultaneous reactions can be combined to perform multistep processes, enabling the use of variable flow rates, reuse of reactors under different conditions, and the storage of intermediates. This fully automated instrument is capable of both linear and convergent syntheses and does not require manual reconfiguration between different processes. The capabilities of this approach are demonstrated by performing optimizations and multistep syntheses of targets, varying concentrations via inline dilutions, exploring several strategies for the multistep synthesis of the anticonvulsant drug rufinamide10, synthesizing eighteen compounds of two derivative libraries that are prepared using different reaction pathways and chemistries, and using the same reagents to perform metallaphotoredox carbon-nitrogen cross-couplings11 in a photochemical module-all without instrument reconfiguration.

Microestimates of wealth for all low- and middle-income countries.

Many critical policy decisions, from strategic investments to the allocation of humanitarian aid, rely on data about the geographic distribution of wealth and poverty. Yet many poverty maps are out of date or exist only at very coarse levels of granularity. Here we develop microestimates of the relative wealth and poverty of the populated surface of all 135 low- and middle-income countries (LMICs) at 2.4 km resolution. The estimates are built by applying machine-learning algorithms to vast and heterogeneous data from satellites, mobile phone networks, and topographic maps, as well as aggregated and deidentified connectivity data from Facebook. We train and calibrate the estimates using nationally representative household survey data from 56 LMICs and then validate their accuracy using four independent sources of household survey data from 18 countries. We also provide confidence intervals for each microestimate to facilitate responsible downstream use. These estimates are provided free for public use in the hope that they enable targeted policy response to the COVID-19 pandemic, provide the foundation for insights into the causes and consequences of economic development and growth, and promote responsible policymaking in support of sustainable development.

Swiss CAT+, a Data-driven Infrastructure for Accelerated Catalysts Discovery and Optimization.

The Catalysis Hub - Swiss CAT+ is a new infrastructure project funded by ETH-domain, co-headed by EPFL and ETHZ. It offers the scientific community a unique integrated technology platform combining automated and high-throughput experimentation with advanced computational data analysis to accelerate the discoveries in the field of sustainable catalytic technologies. Divided into two hubs of expertise, homogeneous catalysis at EPFL and heterogeneous catalysis at ETHZ, the platform is open to academic and private research groups. Following a multi-year investment plan, both hubs have acquired and developed several high-end robotic platforms devoted to the synthesis, characterization, and testing of large numbers of molecular and solid catalysts. The hardware is associated with a fully digitalized experimental workflow and a specific data management strategy to support closed-loop experimentation and advanced computational data analysis.

Catecholase-catalyzed synthesis of wedelolactone, a natural coumestan and its analogs.

Biocatalysis plays an important role in the synthesis of complex organic molecules. Wedelolactone, a natural coumestan, has been reported to have many bioactive properties. A novel and efficient enzyme obtained from sweet potato juice was used for condensation of 4-hydroxycoumarins with catechols to produce wedelolactone and its structurally diverse analogs in moderate to good yields under mild reaction conditions. Hence, this enzymatic approach creates an opportunity to access many coumestan-based compounds that are potential building blocks for the synthesis of pharmaceutically important molecules.

Furan derivatives impair proliferation and affect ultrastructural organization of Trypanosoma cruzi and Leishmania amazonensis.

Chagas disease and leishmaniasis are neglected diseases caused by parasites of the Trypanosomatidae family and together they affect millions of people in the five continents. The treatment of Chagas disease is based on benznidazole, whereas for leishmaniasis few drugs are available, such as amphotericin B and miltefosine. In both cases, the current treatment is not entirely efficient due to toxicity or side effects. Encouraged by the need to discover valid targets and new treatment options, we evaluated 8 furan compounds against Trypanosoma cruzi and Leishmania amazonensis, considering their effects against proliferation, infection, and ultrastructure. Many of them were able to impair T. cruzi and L. amazonensis proliferation, as well as cause ultrastructural alterations, such as Golgi apparatus disorganization, autophagosome formation, and mitochondrial swelling. Taken together, the results obtained so far make these compounds eligible for further steps of chemotherapy study.

A bis-indole/carbazole based C5-curcuminoid fluorescent probe with large Stokes shift for selective detection of biothiols and application to live cell imaging.

A series of heterocyclic C5-curcuminoids (bis(arylmethylidene)acetones) (PJ1-PJ6) having a large Stokes shift (Δλ = 104-173 nm) have been synthesized for the selective detection of cysteine (Cys), homocysteine (Hcy) and glutathione (GSH) in living cells. The compounds were synthesized using a new methodology via deacetylation under microwave conditions. The photophysical properties of these compounds have been studied. Prominent colour changes from bright yellow to colourless in the presence of thiols were observed for PJ1. Live cell imaging has been employed with PJ1 for the utilization of the probe to detect homocysteine in A375 cells and apoptosis in AGS cells.

An Empirical Understanding of the Glycosylation Reaction.

Reliable glycosylation reactions that allow for the stereo- and regioselective installation of glycosidic linkages are paramount to the chemical synthesis of glycan chains. The stereoselectivity of glycosylations is exceedingly difficult to control due to the reaction's high degree of sensitivity and its shifting, simultaneous mechanistic pathways that are controlled by variables of unknown degree of influence, dominance, or interdependency. An automated platform was devised to quickly, reproducibly, and systematically screen glycosylations and thereby address this fundamental problem. Thirteen variables were investigated in as isolated a manner as possible, to identify and quantify inherent preferences of electrophilic glycosylating agents (glycosyl donors) and nucleophiles (glycosyl acceptors). Ways to enhance, suppress, or even override these preferences using judicious environmental conditions were discovered. Glycosylations involving two specific partners can be tuned to produce either 11:1 selectivity of one stereoisomer or 9:1 of the other by merely changing the reaction conditions.

Post-Newtonian Dynamics in Dense Star Clusters: Highly Eccentric, Highly Spinning, and Repeated Binary Black Hole Mergers.

We present models of realistic globular clusters with post-Newtonian dynamics for black holes. By modeling the relativistic accelerations and gravitational-wave emission in isolated binaries and during three- and four-body encounters, we find that nearly half of all binary black hole mergers occur inside the cluster, with about 10% of those mergers entering the LIGO/Virgo band with eccentricities greater than 0.1. In-cluster mergers lead to the birth of a second generation of black holes with larger masses and high spins, which, depending on the black hole natal spins, can sometimes be retained in the cluster and merge again. As a result, globular clusters can produce merging binaries with detectable spins regardless of the birth spins of black holes formed from massive stars. These second-generation black holes would also populate any upper mass gap created by pair-instability supernovae.

LISA Sources in Milky Way Globular Clusters.

We explore the formation of double-compact-object binaries in Milky Way (MW) globular clusters (GCs) that may be detectable by the Laser Interferometer Space Antenna (LISA). We use a set of 137 fully evolved GC models that, overall, effectively match the properties of the observed GCs in the MW. We estimate that, in total, the MW GCs contain ∼21 sources that will be detectable by LISA. These detectable sources contain all combinations of black hole (BH), neutron star, and white dwarf components. We predict ∼7 of these sources will be BH-BH binaries. Furthermore, we show that some of these BH-BH binaries can have signal-to-noise ratios large enough to be detectable at the distance of the Andromeda galaxy or even the Virgo cluster.

Erratum: Binary Black Hole Mergers from Globular Clusters: Implications for Advanced LIGO [Phys. Rev. Lett. 115, 051101 (2015)].

This corrects the article DOI: 10.1103/PhysRevLett.115.051101.

Binary Black Hole Mergers from Globular Clusters: Implications for Advanced LIGO.

The predicted rate of binary black hole mergers from galactic fields can vary over several orders of magnitude and is extremely sensitive to the assumptions of stellar evolution. But in dense stellar environments such as globular clusters, binary black holes form by well-understood gravitational interactions. In this Letter, we study the formation of black hole binaries in an extensive collection of realistic globular cluster models. By comparing these models to observed Milky Way and extragalactic globular clusters, we find that the mergers of dynamically formed binaries could be detected at a rate of ∼100 per year, potentially dominating the binary black hole merger rate. We also find that a majority of cluster-formed binaries are more massive than their field-formed counterparts, suggesting that Advanced LIGO could identify certain binaries as originating from dense stellar environments.

Wrinkling and folding of thin films by viscous stress.

We examine the buckling of a thin elastic film floating on a viscous liquid layer which is itself supported on a prestretched rubber sheet. Releasing the prestretch in the rubber induces a viscous stress in the liquid, which in turn induces a compressive stress in the elastic film, leading to buckling. Unlike many previous studies on wrinkling of floating films, the buckling process in the present study is dominated by viscous effects whereas gravitational effects are negligible. An approximate shear lag model predicts the evolution of the stress profile in the unbuckled film that depends on three parameters: the rate at which the prestretch is released, the thickness of the liquid layer, and the length of the elastic film. A linear perturbation analysis is developed to predict the wavelength of wrinkles. Numerical simulations are conducted to predict nonlinear evolution of the wrinkle wavelength and amplitude. Experiments using elastic polymer films and viscous polymer liquids show trends that are qualitatively consistent with the predictions although quantitatively, the experimentally-observed wrinkle wavelengths are longer than predicted. Although this article is focused only on small-strain wrinkling behavior, we show that application of large nominal strains (on the order of 100%) leads to sharply localized folds. Thus this approach may be useful for developing buckled features with high aspect ratio on surfaces.

Controllable multi-halogenation of a non-native substrate by SyrB2 iron halogenase.

Geminal, multi-halogenated functional groups are widespread in natural products and pharmaceuticals, yet no synthetic methodologies exist that enable selective multi-halogenation of unactivated C-H bonds. Biocatalysts are powerful tools for late-stage C-H functionalization, as they operate with high degrees of regio-, chemo-, and stereoselectivity. 2-oxoglutarate (2OG)-dependent non-heme iron halogenases chlorinate and brominate aliphatic C-H bonds offering a solution for achieving these challenging transformations. Here, we describe the ability of a non-heme iron halogenase, SyrB2, to controllably halogenate non-native substrate alpha-aminobutyric acid (Aba) to yield mono-chlorinated, di-chlorinated, and tri-chlorinated products. These chemoselective outcomes are achieved by controlling the loading of 2OG cofactor and SyrB2 biocatalyst. By using a ferredoxin-based biological reductant for electron transfer to the catalytic center of SyrB2, we demonstrate order-of-magnitude enhancement in the yield of tri-chlorinated product that were previously inaccessible using any single halogenase enzyme. We also apply these strategies to broaden SyrB2's reactivity scope to include multi-bromination and demonstrate chemoenzymatic conversion of the ethyl side chain in Aba to an ethylyne functional group. We show how steric hindrance induced by the successive addition of halogen atoms on Aba's C4 carbon dictates the degree of multi-halogenation by hampering C3-C4 bond rotation within SyrB2's catalytic pocket. Overall, our work showcases the synthetic potential of iron halogenases to facilitate multi-C-H functionalization chemistry.

Newly Synthesized 3-Indolyl Furanoid Inhibits Matrix Metalloproteinase-9 Activity and Prevents Nonsteroidal Anti-inflammatory Drug-Induced Gastric Ulceration.

Indomethacin, a known nonsteroidal anti-inflammatory drug (NSAID) induces gastric inflammation, causing degradation of the extracellular matrix by specific matrix metalloproteinases (MMPs). We investigated the antiulcer efficacy of 3-indolyl furanoids (3g and 3c, i.e., methoxy substitution at 4- and 5-positions of the indole ring, respectively), derived from indomethacin. Interestingly, 3g protected against indomethacin-induced gastropathy in vivo by inhibiting MMP-9. Our work established a chemical modification strategy for the development of safer NSAIDs. Moreover, in vitro and in silico studies confirmed that 3g inhibited MMP-9 activity with an IC50 value of 50 µM by binding to the catalytic cleft of MMP-9, leading to ulcer prevention. Pharmacokinetics was presented as the mean concentration-time profile in the rat plasma, and the extraction efficiency was greater than 70%, showing a Cmax of 104.48 µg/mL after 6.0 h (tmax) treatment with half-life and area under the curve being 7.0 h and 1273.8 h µg/mL, respectively, indicating the higher antiulcer potency of 3g.

Electrostatically regulated active site assembly governs reactivity in non-heme iron halogenases.

Non-heme iron halogenases (NHFe-Hals) catalyze the direct insertion of a chloride/bromide ion at an unactivated carbon position using a high-valent haloferryl intermediate. Despite more than a decade of structural and mechanistic characterization, how NHFe-Hals preferentially bind specific anions and substrates for C-H functionalization remains unknown. Herein, using lysine halogenating BesD and HalB enzymes as model systems, we demonstrate strong positive cooperativity between anion and substrate binding to the catalytic pocket. Detailed computational investigations indicate that a negatively charged glutamate hydrogen-bonded to iron's equatorial-aqua ligand acts as an electrostatic lock preventing both lysine and anion binding in the absence of the other. Using a combination of UV-Vis spectroscopy, binding affinity studies, stopped-flow kinetics investigations, and biochemical assays, we explore the implication of such active site assembly towards chlorination, bromination, and azidation reactivities. Overall, our work highlights previously unknown features regarding how anion-substrate pair binding govern reactivity of iron halogenases that are crucial for engineering next-generation C-H functionalization biocatalysts.

ICB3E induces iNOS expression by ROS-dependent JNK and ERK activation for apoptosis of leukemic cells.

The role of c-Jun N terminal Kinase (JNK) has been well documented in various cellular stresses where it leads to cell death. Similarly, extracellular signal-regulated kinase (ERK) which was identified as a signalling molecule for survival pathway has been shown recently to be involved in apoptosis also. Recently we reported that ICB3E, a synthetic analogue of Piper betle leaf-derived apoptosis-inducing agent hydroxychavicol (HCH), possesses anti-chronic myeloid leukemia (CML) acitivity in vitro and in vivo without insight on mechanism of action. Here we report that ICB3E is three to four times more potent than HCH in inducing apoptosis of leukemic cells without having appreciable effects on normal human peripheral blood mononuclear cells, mouse fibroblast cell line NIH3T3 and monkey kidney epithelial cell line Vero. ICB3E causes early accumulation of mitochondria-derived reactive oxygen species (ROS) in K562 cells. Unlike HCH, ICB3E treatment caused ROS dependent activation of both JNK, ERK and induced the expression of iNOS leading to generation of nitric oxide (NO). This causes cleavage of caspase 9, 3 and PARP leading to apoptosis. Lack of cleavage of caspase 8 and inability of blocking chimera antibody to DR5 or neutralizing antibody to Fas to reverse ICB3E-mediated apoptosis suggest the involvement of only intrinsic pathway. Our data reveal a novel ROS-dependent JNK/ERK-mediated iNOS activation pathway which leads to NO mediated cell death by ICB3E.

Butyrylation Meets Adipogenesis-Probed by a p300-Catalyzed Acylation-Specific Small Molecule Inhibitor: Implication in Anti-obesity Therapy.

The enzyme p300, besides having acetyltransferase activity, can also catalyze other acylation modifications, whose physiological implications are still being investigated. Here, we report that the level of histone butyrylation increases globally as well as locally in the promoters of pro-adipogenic genes during adipogenesis. To delineate the role of p300-catalyzed butyrylation from acetylation in adipogenesis, we identified a semisynthetic derivative (LTK-14A) of garcinol, which specifically inhibited histone butyrylation without affecting acetylation. Treatment of 3T3L1 cells with LTK-14A abolished adipogenesis with downregulation of pro-adipogenic genes along with inhibition of H4K5 butyrylation. Administering LTK-14A to high-fat diet-fed and genetically obese db/db mice led to attenuation/decrease in their weight gain. The reduced obesity could be partially attributed to the inhibition of H4K5 butyrylation in adipocytes and liver. This report therefore not only, for the first time, causally links histone butyrylation with adipogenesis but also presents a probable candidate for anti-obesity therapeutics.

Single Cell Type Specific RNA Isolation and Gene Expression Analysis in Rice Using Laser Capture Microdissection (LCM)-Based Method.

The success of single cell type-specific gene expression or functional study largely depends on the efficient isolation of high-quality RNA from them. Laser capture microdissection (LCM) is an efficient technique that allows accessing and dissecting out a specific individual cell or cell type from a microscopic heterogeneous tissue in a minimally disruptive way. Here, we describe an efficient and inexpensive LCM-based method for the extraction of RNAs with high yield and integrity from laser-microdissected mesophyll and bundle sheath cells of rice leaf. The integrity of isolated RNA is assessed with bioanalyzer analysis, and the presence of mRNA of a specific gene is validated through RT-PCR. This RNA could further be used for uncovering single cell type-specific gene expression signature using next-generation transcriptome sequence or through regular RT-PCR.

Engineering bio-inspired peptide-polyurea hybrids with thermo-responsive shape memory behaviour.

Inspired by Nature's tunability driven by the modulation of structural organization, we utilize peptide motifs as an approach to tailor not only hierarchical structure, but also thermo-responsive shape memory properties of conventional polymeric materials. Specifically, poly(ß-benzyl-L-aspartate)-b-poly(dimethylsiloxane)-b-poly(ß-benzyl-L-aspartate) was incorporated as the soft segment in peptide-polyurea hybrids to manipulate hierarchical ordering through peptide secondary structure and a balance of inter- and intra-molecular hydrogen bonding. Employing these bioinspired peptidic polyureas, we investigated the influence of secondary structure on microphase-separated morphology, and shape fixity and recovery via attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), small-angle X-ray scattering (SAXS) and dynamic mechanical analysis (DMA). The ß-sheet motifs promoted phase mixing through extensive inter-molecular hydrogen bonding between the hard block and peptide segments and provided an increased chain elasticity, resulting in decreased shape fixity compared to a non-peptidic control. In contrast, intra-molecular hydrogen bonding driven by the α-helical arrangements yielded a microphase-separated and hierarchically ordered morphology, leading to an increase in the shape fixing ratio. These results indicate that peptide secondary structure provides a convenient handle for tuning shape memory properties by regulating hydrogen bonding with the surrounding polyurea hard segment, wherein extent of hydrogen bonding and phase mixing between the peptidic block and hard segment dictate the resulting shape memory behaviour. Furthermore, the ability to shift secondary structure as a function of temperature was also demonstrated as a pathway to influence shape memory response. This research highlights that peptide secondary conformation influences the hierarchical ordering and modulates the shape memory response of peptide-polymer hybrids. We anticipate that these findings will enable the design of smart bio-inspired materials with responsive and tailored function via a balance of hydrogen bonding character, structural organization, and mechanics.

Predicting glycosylation stereoselectivity using machine learning.

Predicting the stereochemical outcome of chemical reactions is challenging in mechanistically ambiguous transformations. The stereoselectivity of glycosylation reactions is influenced by at least eleven factors across four chemical participants and temperature. A random forest algorithm was trained using a highly reproducible, concise dataset to accurately predict the stereoselective outcome of glycosylations. The steric and electronic contributions of all chemical reagents and solvents were quantified by quantum mechanical calculations. The trained model accurately predicts stereoselectivities for unseen nucleophiles, electrophiles, acid catalyst, and solvents across a wide temperature range (overall root mean square error 6.8%). All predictions were validated experimentally on a standardized microreactor platform. The model helped to identify novel ways to control glycosylation stereoselectivity and accurately predicts previously unknown means of stereocontrol. By quantifying the degree of influence of each variable, we begin to gain a better general understanding of the transformation, for example that environmental factors influence the stereoselectivity of glycosylations more than the coupling partners in this area of chemical space.