Exceptional capture of methane at low pressure by an iron-based metal-organic framework.

The selective capture of methane (CH4) at low concentrations and its separation from N2 are extremely challenging owing to the weak host-guest interactions between CH4 molecules and any sorbent material. Here, we report the exceptional adsorption of CH4 at low pressure and the efficient separation of CH4/N2 by MFM-300(Fe). MFM-300(Fe) shows a very high uptake for CH4 of 0.85 mmol g-1 at 1 mbar and 298 K and a record CH4/N2 selectivity of 45 for porous solids, representing a new benchmark for CH4 capture and CH4/N2 separation. The excellent separation of CH4/N2 by MFM-300(Fe) has been confirmed by dynamic breakthrough experiments. In situ neutron powder diffraction, and solid-state nuclear magnetic resonance and diffuse reflectance infrared Fourier transform spectroscopies, coupled with modelling, reveal a unique and strong binding of CH4 molecules involving Fe-OH⋯CH4 and C⋯phenyl ring interactions within the pores of MFM-300(Fe), thus promoting the exceptional adsorption of CH4 at low pressure.

SGC-CLK-1: A chemical probe for the Cdc2-like kinases CLK1, CLK2, and CLK4.

Small molecule modulators are important tools to study both basic biology and the complex signaling of protein kinases. The cdc2-like kinases (CLK) are a family of four kinases that have garnered recent interest for their involvement in a diverse set of diseases such as neurodegeneration, autoimmunity, and many cancers. Targeted medicinal chemistry around a CLK inhibitor hit identified through screening of a kinase inhibitor set against a large panel of kinases allowed us to identify a potent and selective inhibitor of CLK1, 2, and 4. Here, we present the synthesis, selectivity, and preliminary biological characterization of this compound - SGC-CLK-1 (CAF-170). We further show CLK2 has the highest binding affinity, and high CLK2 expression correlates with a lower IC50 in a screen of multiple cancer cell lines. Finally, we show that SGC-CLK-1 not only reduces serine arginine-rich (SR) protein phosphorylation but also alters SR protein and CLK2 subcellular localization in a reversible way. Therefore, we anticipate that this compound will be a valuable tool for increasing our understanding of CLKs and their targets, SR proteins, at the level of phosphorylation and subcellular localization.

Direct Conversion of Methane to Ethylene and Acetylene over an Iron-Based Metal-Organic Framework.

Conversion of methane (CH4) to ethylene (C2H4) and/or acetylene (C2H2) enables routes to a wide range of products directly from natural gas. However, high reaction temperatures and pressures are often required to activate and convert CH4 controllably, and separating C2+ products from unreacted CH4 can be challenging. Here, we report the direct conversion of CH4 to C2H4 and C2H2 driven by non-thermal plasma under ambient (25 °C and 1 atm) and flow conditions over a metal-organic framework material, MFM-300(Fe). The selectivity for the formation of C2H4 and C2H2 reaches 96% with a high time yield of 334 µmol gcat-1 h-1. At a conversion of 10%, the selectivity to C2+ hydrocarbons and time yield exceed 98% and 2056 µmol gcat-1 h-1, respectively, representing a new benchmark for conversion of CH4. In situ neutron powder diffraction, inelastic neutron scattering and solid-state nuclear magnetic resonance, electron paramagnetic resonance (EPR), and diffuse reflectance infrared Fourier transform spectroscopies, coupled with modeling studies, reveal the crucial role of Fe-O(H)-Fe sites in activating CH4 and stabilizing reaction intermediates via the formation of an Fe-O(CH3)-Fe adduct. In addition, a cascade fixed-bed system has been developed to achieve online separation of C2H4 and C2H2 from unreacted CH4 for direct use. Integrating the processes of CH4 activation, conversion, and product separation within one system opens a new avenue for natural gas utility, bridging the gap between fundamental studies and practical applications in this area.

High-content live-cell multiplex screen for chemogenomic compound annotation based on nuclear morphology.

Well-characterized small molecules enable the study of cell processes and facilitate target validation. Here, we describe a high-content multiplex screen to investigate cell viability over 48 h, which can be combined with investigating phenotypic features, such as tubulin binding and mitochondrial content, as initial cellular quality control of diverse compounds. The protocol is on a live-cell basis and easily adaptable and scalable. It details cell preparation, compound handling, plate layout configuration, image acquisition with the CQ1, and data analysis using the CellPathfinder software. For complete details on the use and execution of this protocol, please refer to Tjaden et al. (2022).

Direct photo-oxidation of methane to methanol over a mono-iron hydroxyl site.

Natural gas, consisting mainly of methane (CH4), has a relatively low energy density at ambient conditions (~36 kJ l-1). Partial oxidation of CH4 to methanol (CH3OH) lifts the energy density to ~17 MJ l-1 and drives the production of numerous chemicals. In nature, this is achieved by methane monooxygenase with di-iron sites, which is extremely challenging to mimic in artificial systems due to the high dissociation energy of the C-H bond in CH4 (439 kJ mol-1) and facile over-oxidation of CH3OH to CO and CO2. Here we report the direct photo-oxidation of CH4 over mono-iron hydroxyl sites immobilized within a metal-organic framework, PMOF-RuFe(OH). Under ambient and flow conditions in the presence of H2O and O2, CH4 is converted to CH3OH with 100% selectivity and a time yield of 8.81 ± 0.34 mmol gcat-1 h-1 (versus 5.05 mmol gcat-1 h-1 for methane monooxygenase). By using operando spectroscopic and modelling techniques, we find that confined mono-iron hydroxyl sites bind CH4 by forming an [Fe-OH···CH4] intermediate, thus lowering the barrier for C-H bond activation. The confinement of mono-iron hydroxyl sites in a porous matrix demonstrates a strategy for C-H bond activation in CH4 to drive the direct photosynthesis of CH3OH.

Image-Based Annotation of Chemogenomic Libraries for Phenotypic Screening.

Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still pose a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, we report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.

Technical performance and reproducibility following rotational atherectomy of femoropopliteal artery occlusive lesions: analysis of the multicenter MORPHEAS Registry.

BACKGROUND: The purpose of this study was to define patient and anatomical factors associated with technical results specific to rotational atherectomy. Controversy exists surrounding appropriate utilization of atherectomy to treat femoral-popliteal atherosclerosis. Importantly, the existence of different atherectomy devices and lack of technical reports highlighting variables that impact outcomes obscures the ability to assess perioperative performance. METHODS: The nonindustry sponsored, Multicentric National Registry on the use of rotational atherectomy in femoral-popliteal occlusive atherosclerotic disease (MORPHEAS) database was queried. The MORPHEAS investigators included experienced providers at four centers who previously had not utilized rotational atherectomy. The primary endpoint was flow-limiting dissection and/or >50% recoil resulting in stent-placement while a secondary endpoint included peripheral thromboembolism incidence. RESULTS: One hundred thirteen patients were enrolled. Only femoropopliteal occlusions were included in the analysis and anatomic distribution and calcification severity were depicted separately. The most common adjunctive therapy was drug-coated balloon angioplasty (84%; N.=96). Flow-limiting dissection was identified in 16% (N.=18) and thromboembolism occurred in 4% (N.=4). Diabetes increased risk of thromboembolism (P=0.03) while lesion length ≥8.0 cm (P=0.07) and SFA-popliteal adductor canal location (P=0.01) were associated with flow-limiting dissection. In multivariable analysis, SFA-popliteal adductor canal occlusion had a 4.7-fold risk of perioperative complications (OR=4.7, 95%CI: 1.1-21.0; P=0.04). CONCLUSIONS: Rotational atherectomy was characterized by reproducible performance among four centers; however, diabetic patients, as well as those with long-segment, heavily calcified SFA-popliteal adductor canal occlusion present greatest risk of complications.

Discovery of a Potent and Highly Isoform-Selective Inhibitor of the Neglected Ribosomal Protein S6 Kinase Beta 2 (S6K2).

The ribosomal protein S6 kinase beta 2 (S6K2) is thought to play an important role in malignant cell proliferation, but is understudied compared to its closely related homolog S6 kinase beta 1 (S6K1). To better understand the biological function of S6K2, chemical probes are needed, but the high similarity between S6K2 and S6K1 makes it challenging to selectively address S6K2 with small molecules. We were able to design the first potent and highly isoform-specific S6K2 inhibitor from a known S6K1-selective inhibitor, which was merged with a covalent inhibitor engaging a cysteine located in the hinge region in the fibroblast growth factor receptor kinase (FGFR) 4 via a nucleophilic aromatic substitution (SNAr) reaction. The title compound shows a high selectivity over kinases with an equivalently positioned cysteine, as well as in a larger kinase panel. A good stability towards glutathione and Nα-acetyl lysine indicates a non-promiscuous reactivity pattern. Thus, the title compound represents an important step towards a high-quality chemical probe to study S6K2-specific signaling.

Design and Development of a Chemical Probe for Pseudokinase Ca2+/calmodulin-Dependent Ser/Thr Kinase.

CASK (Ca2+/calmodulin-dependent Ser/Thr kinase) is a member of the MAGUK (membrane-associated guanylate kinase) family that functions as neurexin kinases with roles implicated in neuronal synapses and trafficking. The lack of a canonical DFG motif, which is altered to GFG in CASK, led to the classification as a pseudokinase. However, functional studies revealed that CASK can still phosphorylate substrates in the absence of divalent metals. CASK dysfunction has been linked to many diseases, including colorectal cancer, Parkinson's disease, and X-linked mental retardation, suggesting CASK as a potential drug target. Here, we exploited structure-based design for the development of highly potent and selective CASK inhibitors based on 2,4-diaminopyrimidine-5-carboxamides targeting an unusual pocket created by the GFG motif. The presented inhibitor design offers a more general strategy for the development of pseudokinase ligands that harbor unusual sequence motifs. It also provides a first chemical probe for studying the biological roles of CASK.

Development of a Selective Dual Discoidin Domain Receptor (DDR)/p38 Kinase Chemical Probe.

Discoidin domain receptors 1 and 2 (DDR1/2) play a central role in fibrotic disorders, such as renal and pulmonary fibrosis, atherosclerosis, and various forms of cancer. Potent and selective inhibitors, so-called chemical probe compounds, have been developed to study DDR1/2 kinase signaling. However, these inhibitors showed undesired activity on other kinases such as the tyrosine protein kinase receptor TIE or tropomyosin receptor kinases, which are related to angiogenesis and neuronal toxicity. In this study, we optimized our recently published p38 mitogen-activated protein kinase inhibitor 7 toward a potent and cell-active dual DDR/p38 chemical probe and developed a structurally related negative control. The structure-guided design approach used provided insights into the P-loop folding process of p38 and how targeting of non-conserved amino acids modulates inhibitor selectivity. The developed and comprehensively characterized DDR/p38 probe, 30 (SR-302), is a valuable tool for studying the role of DDR kinase in normal physiology and in disease development.

Assessing reversible and irreversible binding effects of kinase covalent inhibitors through ADP-Glo assays.

Typical enzymatic inhibition assays often demonstrate improved potency for kinase covalent inhibitors compared to reversible inhibitors. This can primarily be attributed to the irreversible mode of action and could affect the evaluations of the ATP-competitive nature of covalent inhibitors, hindering optimization of these compounds. Here, we describe a version of ADP-Glo assay, in which modification of inhibitor incubation time in the presence or absence of ATP enables a quick assessment of relative reversible and irreversible effects of kinase covalent inhibitors. For complete details on the use and execution of this protocol, please refer to Schröder et al. (2020).

Purification of Propylene and Ethylene by a Robust Metal-Organic Framework Mediated by Host-Guest Interactions.

Industrial purification of propylene and ethylene requires cryogenic distillation and selective hydrogenation over palladium catalysts to remove propane, ethane and/or trace amounts of acetylene. Here, we report the excellent separation of equimolar mixtures of propylene/propane and ethylene/ethane, and of a 1/100 mixture of acetylene/ethylene by a highly robust microporous material, MFM-520, under dynamic conditions. In situ synchrotron single crystal X-ray diffraction, inelastic neutron scattering and analysis of adsorption thermodynamic parameters reveal that a series of synergistic host-guest interactions involving hydrogen bonding and π⋅⋅⋅π stacking interactions underpin the cooperative binding of alkenes within the pore. Notably, the optimal pore geometry of the material enables selective accommodation of acetylene. The practical potential of this porous material has been demonstrated by fabricating mixed-matrix membranes comprising MFM-520, Matrimid and PIM-1, and these exhibit not only a high permeability for propylene (≈1984 Barrer), but also a separation factor of 7.8 for an equimolar mixture of propylene/propane at 298 K.

Selective Gas Uptake and Rotational Dynamics in a (3,24)-Connected Metal-Organic Framework Material.

The desolvated (3,24)-connected metal-organic framework (MOF) material, MFM-160a, [Cu3(L)(H2O)3] [H6L = 1,3,5-triazine-2,4,6-tris(aminophenyl-4-isophthalic acid)], exhibits excellent high-pressure uptake of CO2 (110 wt% at 20 bar, 298 K) and highly selective separation of C2 hydrocarbons from CH4 at 1 bar pressure. Henry's law selectivities of 79:1 for C2H2:CH4 and 70:1 for C2H4:CH4 at 298 K are observed, consistent with ideal adsorption solution theory (IAST) predictions. Significantly, MFM-160a shows a selectivity of 16:1 for C2H2:CO2. Solid-state 2H NMR spectroscopic studies on partially deuterated MFM-160-d12 confirm an ultra-low barrier (∼2 kJ mol-1) to rotation of the phenyl group in the activated MOF and a rotation rate 5 orders of magnitude slower than usually observed for solid-state materials (1.4 × 106 Hz cf. 1011-1013 Hz). Upon introduction of CO2 or C2H2 into desolvated MFM-160a, this rate of rotation was found to increase with increasing gas pressure, a phenomenon attributed to the weakening of an intramolecular hydrogen bond in the triazine-containing linker upon gas binding. DFT calculations of binding energies and interactions of CO2 and C2H2 around the triazine core are entirely consistent with the 2H NMR spectroscopic observations.

Discovery of a Novel Class of Covalent Dual Inhibitors Targeting the Protein Kinases BMX and BTK.

The nonreceptor tyrosine TEC kinases are key regulators of the immune system and play a crucial role in the pathogenesis of diverse hematological malignancies. In contrast to the substantial efforts in inhibitor development for Bruton's tyrosine kinase (BTK), specific inhibitors of the other TEC kinases, including the bone marrow tyrosine kinase on chromosome X (BMX), remain sparse. Here we present a novel class of dual BMX/BTK inhibitors, which were designed from irreversible inhibitors of Janus kinase (JAK) 3 targeting a cysteine located within the solvent-exposed front region of the ATP binding pocket. Structure-guided design exploiting the differences in the gatekeeper residues enabled the achievement of high selectivity over JAK3 and certain other kinases harboring a sterically demanding residue at this position. The most active compounds inhibited BMX and BTK with apparent IC50 values in the single digit nanomolar range or below showing moderate selectivity within the TEC family and potent cellular target engagement. These compounds represent an important first step towards selective chemical probes for the protein kinase BMX.

Crystal Structure and Inhibitor Identifications Reveal Targeting Opportunity for the Atypical MAPK Kinase ERK3.

Extracellular signal-regulated kinase 3 (ERK3), known also as mitogen-activated protein kinase 6 (MAPK6), is an atypical member of MAPK kinase family, which has been poorly studied. Little is known regarding its function in biological processes, yet this atypical kinase has been suggested to play important roles in the migration and invasiveness of certain cancers. The lack of tools, such as a selective inhibitor, hampers the study of ERK3 biology. Here, we report the crystal structure of the kinase domain of this atypical MAPK kinase, providing molecular insights into its distinct ATP binding pocket compared to the classical MAPK ERK2, explaining differences in their inhibitor binding properties. Medium-scale small molecule screening identified a number of inhibitors, several of which unexpectedly exhibited remarkably high inhibitory potencies. The crystal structure of CLK1 in complex with CAF052, one of the most potent inhibitors identified for ERK3, revealed typical type-I binding mode of the inhibitor, which by structural comparison could likely be maintained in ERK3. Together with the presented structural insights, these diverse chemical scaffolds displaying both reversible and irreversible modes of action, will serve as a starting point for the development of selective inhibitors for ERK3, which will be beneficial for elucidating the important functions of this understudied kinase.

Selective targeting of the αC and DFG-out pocket in p38 MAPK.

The p38 MAPK cascade is a key signaling pathway linked to a multitude of physiological functions and of central importance in inflammatory and autoimmune diseases. Although studied extensively, little is known about how conformation-specific inhibitors alter signaling outcomes. Here, we have explored the highly dynamic back pocket of p38 MAPK with allosteric urea fragments. However, screening against known off-targets showed that these fragments maintained the selectivity issues of their parent compound BIRB-796, while combination with the hinge-binding motif of VPC-00628 greatly enhanced inhibitor selectivity. Further efforts focused therefore on the exploration of the αC-out pocket of p38 MAPK, yielding compound 137 as a highly selective type-II inhibitor. Even though 137 is structurally related to a recent p38 type-II chemical probe, SR-318, the data presented here provide valuable insights into back-pocket interactions that are not addressed in SR-318 and it provides an alternative chemical tool with good cellular activity targeting also the p38 back pocket.

PROTAC-mediated degradation reveals a non-catalytic function of AURORA-A kinase.

The mitotic kinase AURORA-A is essential for cell cycle progression and is considered a priority cancer target. Although the catalytic activity of AURORA-A is essential for its mitotic function, recent reports indicate an additional non-catalytic function, which is difficult to target by conventional small molecules. We therefore developed a series of chemical degraders (PROTACs) by connecting a clinical kinase inhibitor of AURORA-A to E3 ligase-binding molecules (for example, thalidomide). One degrader induced rapid, durable and highly specific degradation of AURORA-A. In addition, we found that the degrader complex was stabilized by cooperative binding between AURORA-A and CEREBLON. Degrader-mediated AURORA-A depletion caused an S-phase defect, which is not the cell cycle effect observed upon kinase inhibition, supporting an important non-catalytic function of AURORA-A during DNA replication. AURORA-A degradation induced rampant apoptosis in cancer cell lines and thus represents a versatile starting point for developing new therapeutics to counter AURORA-A function in cancer.

p63 uses a switch-like mechanism to set the threshold for induction of apoptosis.

The p53 homolog TAp63α is the transcriptional key regulator of genome integrity in oocytes. After DNA damage, TAp63α is activated by multistep phosphorylation involving multiple phosphorylation events by the kinase CK1, which triggers the transition from a dimeric and inactive conformation to an open and active tetramer that initiates apoptosis. By measuring activation kinetics in ovaries and single-site phosphorylation kinetics in vitro with peptides and full-length protein, we show that TAp63α phosphorylation follows a biphasic behavior. Although the first two CK1 phosphorylation events are fast, the third one, which constitutes the decisive step to form the active conformation, is slow. Structure determination of CK1 in complex with differently phosphorylated peptides reveals the structural mechanism for the difference in the kinetic behavior based on an unusual CK1/TAp63α substrate interaction in which the product of one phosphorylation step acts as an inhibitor for the following one.

HighVia-A Flexible Live-Cell High-Content Screening Pipeline to Assess Cellular Toxicity.

High-content screening to monitor disease-modifying phenotypes upon small-molecule addition has become an essential component of many drug and target discovery platforms. One of the most common phenotypic approaches, especially in the field of oncology research, is the assessment of cell viability. However, frequently used viability readouts employing metabolic proxy assays based on homogeneous colorimetric/fluorescent reagents are one-dimensional, provide limited information, and can in many cases yield conflicting or difficult-to-interpret results, leading to misinterpretation of data and wasted resources.The resurgence of high-content, phenotypic screening has significantly improved the quality and breadth of cell viability data, which can be obtained at the very earliest stages of drug and target discovery. Here, we describe a relatively inexpensive, high-throughput, high-content, multiparametric, fluorescent imaging protocol using a live-cell method of three fluorescent probes (Hoechst, Yo-Pro-3, and annexin V), that is amenable to the addition of further fluorophores. The protocol enables the accurate description and profiling of multiple cell death mechanisms, including apoptosis and necrosis, as well as accurate determination of compound IC50, and has been validated on a range of high-content imagers and image analysis software. To validate the protocol, we have used a small library of approximately 200 narrow-spectrum kinase inhibitors and clinically approved drugs. This fully developed, easy-to-use pipeline has subsequently been implemented in several academic screening facilities, yielding fast, flexible, and rich cell viability data for a range of early-stage high-throughput drug and target discovery programs.