Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog.

B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.

Binding kinetics of quaternary ammonium ions in Kcv potassium channels.

Kcv channels from plant viruses represent the autonomous pore module of potassium channels, devoid of any regulatory domains. These small proteins show very reproducible single-channel behavior in planar lipid bilayers. Thus, they are an optimum system for the study of the biophysics of ion transport and gating. Structural models based on homology modeling have been used successfully, but experimental structural data are currently not available. Here we determine the size of the cytosolic pore entrance by studying the blocker kinetics. Blocker binding and dissociation rate constants ranging from 0.01 to 1000 ms-1 were determined for different quaternary ammonium ions. We found that the cytosolic pore entrance of KcvNTS must be at least 11 Å wide. The results further indicate that the residues controlling a cytosolic gate in one of the Kcv isoforms influence blocker binding/dissociation as well as a second gate even when the cytosolic gate is in the open state. The voltage dependence of the rate constant of blocker release is used to test, which blockers bind to the same binding site.

3-Amino-pyrazolo[3,4-d]pyrimidines as p38α kinase inhibitors: design and development to a highly selective lead.

Learnings from previous Roche p38-selective inhibitors were applied to a new fragment hit, which was optimized to a potent, exquisitely selective preclinical lead with a good pharmacokinetic profile.

Asymmetric Interplay Between K+ and Blocker and Atomistic Parameters From Physiological Experiments Quantify K+ Channel Blocker Release.

Modulating the activity of ion channels by blockers yields information on both the mode of drug action and on the biophysics of ion transport. Here we investigate the interplay between ions in the selectivity filter (SF) of K+ channels and the release kinetics of the blocker tetrapropylammonium in the model channel KcvNTS. A quantitative expression calculates blocker release rate constants directly from voltage-dependent ion occupation probabilities in the SF. The latter are obtained by a kinetic model of single-channel currents recorded in the absence of the blocker. The resulting model contains only two adjustable parameters of ion-blocker interaction and holds for both symmetric and asymmetric ionic conditions. This data-derived model is corroborated by 3D reference interaction site model (3D RISM) calculations on several model systems, which show that the K+ occupation probability is unaffected by the blocker, a direct consequence of the strength of the ion-carbonyl attraction in the SF, independent of the specific protein background. Hence, KcvNTS channel blocker release kinetics can be reduced to a small number of system-specific parameters. The pore-independent asymmetric interplay between K+ and blocker ions potentially allows for generalizing these results to similar potassium channels.

Extensive Embolization of Splanchnic Artery Aneurysms due to Segmental Arterial Mediolysis. / Extensive Embolisation von Aneurysmata der Viszeral-Arterien bei segmentaler arterieller Mediolyse.

AIM: Segmental arterial mediolysis (SAM) is a rare non-atherosclerotic, non-inflammatory, non-infectious arteriopathy in middle-aged patients that tends to affect medium-sized splanchnic arteries typically leading to dissecting aneurysms which in case of rupture have a high mortality. Treatment options include watchful waiting and endovascular or surgical intervention. There are no official treatment guidelines and to the best of our knowledge, there has not been any report of extensive exclusion of multiple splanchnic vessel regions in affected patients to date. MATERIALS AND METHODS: We retrospectively examined the outcome of extensive splanchnic embolization in four patients suffering from SAM between 2011 and 2016 with follow-up periods of up to 7 years. RESULTS: One patient presented with abdominal pain due to rupture of aneurysms of the pancreaticoduodenal arcade, one with abdominal pain due to dissection, and two were clinically asymptomatic but displayed rapidly progressing disease over the course of 12 months. All patients were treated with complete exclusion of the diseased vessel segments by coiling all branches to and from the diseased segment. In three cases the main hepatic artery was excluded completely. In one case, the complete vascular bed of the celiac axis was excluded by coiling the distal vessel branches and placing a stent graft over the orifice of the celiac trunk. During a follow-up period of a minimum of 2 and a maximum of 7 years after intervention, there were no immediate or long-term complications except for a temporary arterio-portal fistula. Interestingly, no new diseased areas of SAM were detected afterwards. CONCLUSION: Extensive endovascular exclusion of the entire diseased arterial segment with coils seems to be a safe and effective treatment option in patients with SAM presenting with ruptured or rapidly growing aneurysms. Provided that patients have normal liver function and proper portal venous flow, risk of hepatobiliary complications seems to be low even after extensive embolization. KEY POINTS: · An asymptomatic SAM can be followed up.. · In case of disease progression or suspicion of aneurysm rupture, an endovascular approach is indicated where the whole pathological vessel bed should be excluded with coils.. · It seems that exclusion of even extensive vessel areas is tolerated.. CITATION FORMAT: · Najafi A, Sheikh GT, Binkert C. Extensive Embolization of Splanchnic Artery Aneurysms due to Segmental Arterial Mediolysis. Fortschr Röntgenstr 2019; 191: 1010 - 1014.

Outcome of Nellix-EVAS: single center mid-term results.

BACKGROUND: Endovascular aortic sealing (EVAS) using the Nellix system was a new approach to reduce the frequency of type II endoleaks after endovascular aortic repair. We analyzed the mid-term results, specifically looking at device migration, endoleaks and subsequent necessary secondary interventions. RESULTS: Ten patients underwent elective EVAS treatment during our study period. 7 patients were within the IFU while 3 patients had a proximal neck shorter than 10 mm. Technical success rate was 100% and there were no short-term vascular complications. One patient died from urosepsis 14 days after the procedure and was excluded from further analysis. A total of 6 out of 9 patients (67%) experienced device complications such as proximal graft kinking, limb separation or caudal migration. 5 also showed type Ia endoleak. DISCUSSION: While no complication occurred short-term (up to 12 months), the Nellix system showed a high percentage of limb separation, caudal graft migration, and type Ia endoleak on mid-term follow-up, likely due to insufficient proximal anchoring of the device. Possible salvage treatments are discussed.

Discovery of Asciminib (ABL001), an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1.

Chronic myelogenous leukemia (CML) arises from the constitutive activity of the BCR-ABL1 oncoprotein. Tyrosine kinase inhibitors (TKIs) that target the ATP-binding site have transformed CML into a chronic manageable disease. However, some patients develop drug resistance due to ATP-site mutations impeding drug binding. We describe the discovery of asciminib (ABL001), the first allosteric BCR-ABL1 inhibitor to reach the clinic. Asciminib binds to the myristate pocket of BCR-ABL1 and maintains activity against TKI-resistant ATP-site mutations. Although resistance can emerge due to myristate-site mutations, these are sensitive to ATP-competitive inhibitors so that combinations of asciminib with ATP-competitive TKIs suppress the emergence of resistance. Fragment-based screening using NMR and X-ray yielded ligands for the myristate pocket. An NMR-based conformational assay guided the transformation of these inactive ligands into ABL1 inhibitors. Further structure-based optimization for potency, physicochemical, pharmacokinetic, and drug-like properties, culminated in asciminib, which is currently undergoing clinical studies in CML patients.

Laser Cladding of Ultra-Thin Nickel-Based Superalloy Sheets.

Laser cladding is a well-established process to apply coatings on metals. However, on substrates considerably thinner than 1 mm it is only rarely described in the literature. In this work 200 µm thin sheets of nickel-based superalloy 718 are coated with a powder of a cobalt-based alloy, Co-28Cr-9W-1.5Si, by laser cladding. The process window is very narrow, therefore, a precisely controlled Yb fiber laser was used. To minimize the input of energy into the substrate, lines were deposited by setting single overlapping points. In a design of experiments (DoE) study, the process parameters of laser power, laser spot area, step size, exposure time, and solidification time were varied and optimized by examining the clad width, weld penetration, and alloying depth. The microstructure of the samples was investigated by optical microscope (OM) and scanning electron microscopy (SEM), combined with electron backscatter diffraction (EBSD) and energy dispersive X-ray spectroscopy (EDX). Similarly to laser cladding of thicker substrates, the laser power shows the highest influence on the resulting clad. With a higher laser power, the clad width and alloying depth increase, and with a larger laser spot area the weld penetration decreases. If the process parameters are controlled precisely, laser cladding of such thin sheets is manageable.

Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.

PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small molecules targeting EZH2 was shown to result in antitumor efficacy. Here, we describe the optimization of a chemical series representing a new class of PRC2 inhibitors which acts allosterically via the trimethyllysine pocket of the noncatalytic EED subunit. Deconstruction of a larger and complex screening hit to a simple fragment-sized molecule followed by structure-guided regrowth and careful property modulation were employed to yield compounds which achieve submicromolar inhibition in functional assays and cellular activity. The resulting molecules can serve as a simplified entry point for lead optimization and can be utilized to study this new mechanism of PRC2 inhibition and the associated biology in detail.

Discovery of First-in-Class, Potent, and Orally Bioavailable Embryonic Ectoderm Development (EED) Inhibitor with Robust Anticancer Efficacy.

Overexpression and somatic heterozygous mutations of EZH2, the catalytic subunit of polycomb repressive complex 2 (PRC2), are associated with several tumor types. EZH2 inhibitor, EPZ-6438 (tazemetostat), demonstrated clinical efficacy in patients with acceptable safety profile as monotherapy. EED, another subunit of PRC2 complex, is essential for its histone methyltransferase activity through direct binding to trimethylated lysine 27 on histone 3 (H3K27Me3). Herein we disclose the discovery of a first-in-class potent, selective, and orally bioavailable EED inhibitor compound 43 (EED226). Guided by X-ray crystallography, compound 43 was discovered by fragmentation and regrowth of compound 7, a PRC2 HTS hit that directly binds EED. The ensuing scaffold hopping followed by multiparameter optimization led to the discovery of 43. Compound 43 induces robust and sustained tumor regression in EZH2MUT preclinical DLBCL model. For the first time we demonstrate that specific and direct inhibition of EED can be effective as an anticancer strategy.

Pathway to the clinic: inhibition of P38 MAP kinase. A review of ten chemotypes selected for development.

p38 mitogen activated protein (MAP) kinase remains the most compelling therapeutic target for oral drug intervention for a wide range of autoimmune disorders based on the central role this enzyme plays in inflammatory cell signaling. Efforts to discover inhibitors of p38 suitable for clinical investigation have continued to escalate in part due to the incredible diversity of unique chemotypes reported to inhibit the enzyme. Since 1993, at least seventeen p38 inhibitors have been reported to have entered into clinical trials. Next generation inhibitors have been disclosed with improved potency for p38 and enhanced selectivity versus other protein kinases. Over the last three years, there have been multiple reports of cytokine suppression in humans following oral administration of p38 inhibitors. These results, in addition to proof of concept studies in rheumatoid patients, have established p38 inhibition as an avenue for the future management of pro-inflammatory cytokine based diseases. This review describes the discovery at Roche of novel p38 inhibitors which have advanced into clinical trials. The pharmacology of the Roche compounds is then compared with eight chemically distinct p38 inhibitors known to have entered clinical development.

Structure-based drug design of RN486, a potent and selective Bruton's tyrosine kinase (BTK) inhibitor, for the treatment of rheumatoid arthritis.

Structure-based drug design was used to guide the optimization of a series of selective BTK inhibitors as potential treatments for Rheumatoid arthritis. Highlights include the introduction of a benzyl alcohol group and a fluorine substitution, each of which resulted in over 10-fold increase in activity. Concurrent optimization of drug-like properties led to compound 1 (RN486) ( J. Pharmacol. Exp. Ther. 2012 , 341 , 90 ), which was selected for advanced preclinical characterization based on its favorable properties.

Discovery of 6-(2,4-difluorophenoxy)-2-[3-hydroxy-1-(2-hydroxyethyl)propylamino]-8-methyl-8H-pyrido[2,3-d]pyrimidin-7-one (pamapimod) and 6-(2,4-difluorophenoxy)-8-methyl-2-(tetrahydro-2H-pyran-4-ylamino)pyrido[2,3-d]pyrimidin-7(8H)-one (R1487) as orally bioavailable and highly selective inhibitors of p38α mitogen-activated protein kinase.

The development of a new series of p38α inhibitors resulted in the identification of two clinical candidates, one of which was advanced into a phase 2 clinical study for rheumatoid arthritis. The original lead, an lck inhibitor that also potently inhibited p38α, was a screening hit from our kinase inhibitor library. This manuscript describes the optimization of the lead to p38-selective examples with good pharmacokinetic properties.