Deubiquitinase-targeting chimeras for targeted protein stabilization.

Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS.

Performance and cost-benefit analysis of anaerobic moving bed biofilm reactor for pretreatment of textile wastewater.

Performance of an anaerobic moving bed biofilm reactor (AnMBBR) was evaluated for pretreatment of real textile desizing wastewater at organic loading rate (OLR) of 1±0.05 to 6.3±0.37 kgCOD/m3/d. After OLR optimization, the performance of AnMBBR was evaluated for biodegradation of reactive dyes. AnMBBR was operated under a mesophilic temperature range of 30 to 36 °C, while the oxidation-reduction potential (ORP) and pH were in the range of 504 to 594 (-mV) and 6.98 to 7.28, respectively. By increasing the OLR from 1±0.05 to 6.3±0.37 kgCOD/m3/d, COD and BOD5 removal was decreased from 84 to 39% and 89 to 49%, respectively. While the production of biogas was increased from 0.12 to 0.83 L/L·d up to an optimum OLR of 4.9±0.43 kgCOD/m3/d. With increase in the dye concentration in the feed, COD, BOD5, color removal and biogas production reduced from 56, 63, 70% and 0.65 L/L·d to 34, 43, 41% and 0.08 L/L·d, respectively. Based on the data obtained, a cost-benefit analysis of AnMBBR was also investigated for the pretreatment of real textile desizing wastewater. Cost estimation of anaerobic pretreatment of textile desizing wastewater indicated a net profit of 21.09 million PKR/yr (114,000 €/yr) and a potential payback period of 2.54 years.

Author Correction: Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex.

The anticancer agent indisulam inhibits cell proliferation by causing degradation of RBM39, an essential mRNA splicing factor. Indisulam promotes an interaction between RBM39 and the DCAF15 E3 ligase substrate receptor, leading to RBM39 ubiquitination and proteasome-mediated degradation. To delineate the precise mechanism by which indisulam mediates the DCAF15-RBM39 interaction, we solved the DCAF15-DDB1-DDA1-indisulam-RBM39(RRM2) complex structure to a resolution of 2.3 Å. DCAF15 has a distinct topology that embraces the RBM39(RRM2) domain largely via non-polar interactions, and indisulam binds between DCAF15 and RBM39(RRM2), coordinating additional interactions between the two proteins. Studies with RBM39 point mutants and indisulam analogs validated the structural model and defined the RBM39 α-helical degron motif. The degron is found only in RBM23 and RBM39, and only these proteins were detectably downregulated in indisulam-treated HCT116 cells. This work further explains how indisulam induces RBM39 degradation and defines the challenge of harnessing DCAF15 to degrade additional targets.

Functional Mesostructured Electrospun Polymer Nonwovens with Supramolecular Nanofibers.

Functional, hierarchically mesostructured nonwovens are of fundamental importance because complex fiber morphologies increase the active surface area and functionality allowing for the effective immobilization of metal nanoparticles. Such complex functional fiber morphologies clearly widen the property profile and enable the preparation of more efficient and selective filter media. Here, the realization of hierarchically mesostructured nonwovens with barbed wire-like morphology is demonstrated by combining electrospun polystyrene fibers, decorated with patchy worm-like micelles, with solution-processed supramolecular short fibers composed of 1,3,5-benzenetricarboxamides with peripheral N,N-diisopropylaminoethyl substituents. The worm-like micelles with a patchy microphase-separated corona are prepared by crystallization-driven self-assembly of a polyethylene based triblock terpolymer and deposited on top of the polystyrene fibers by coaxial electrospinning. The micelles are designed in a way that their patches promote the directed self-assembly of the 1,3,5-benzenetricarboxamide and the fixation of the supramolecular nanofibers on the supporting polystyrene fibers. Functionality of the mesostructured nonwoven is provided by the peripheral N,N-diisopropylaminoethyl substituents of the 1,3,5-benzenetricarboxamide and proven by the effective immobilization of individual palladium nanoparticles on the supramolecular nanofibers. The preparation of hierarchically mesostructured nonwovens and their shown functionality demonstrate that such systems are attractive candidates to be used for example in filtration, selective separation and heterogenous catalysis.

Thickness sensor for drying paints using THz spectroscopy.

Optical terahertz technology has, despite its exciting properties, such as transparency of visibly opaque materials, 30 years after its technological breakthrough, not found a widespread application with societal relevance. Main causes are its maturity and costs. If, however, the uniqueness of both THz radiation and time-domain spectroscopy is used to close a technological gap in the right market sector, we here show that successful applications are in reach. We have chosen the automotive industry, where the optimization of coatings applied in the paint shop is of longstanding concern for this most expensive unit of the car production line. Here we report on the development of a THz-based sensor system. We study the light-matter interaction of drying polymer coatings and use advanced novel signal processing algorithms to determine the state of matter of drying paints. This very first sensor system for the inspection of wet coatings that accurately predicts the eventual dry thickness without requiring paint-type calibration. Industrial robustness is guaranteed by a bespoke optical beam design. Our sensor demonstrator outperforms state-of-the-art thickness sensors applied on dry coatings by a factor three and is expected to become a game changer for the paint shop, where today's scrap rates worldwide are as high as one car body per minute.

Visualization of the epimysium and fascia thoracolumbalis at the lumbar spine using MRI.

BACKGROUND: The fascia thoracolumbalis (FTL) is an important component for stabilization and motion control of the lumbar spine. It coordinates the traction forces of the autochthonous muscles of the back (AM) and connects them to the muscles of the abdominal wall, shoulder, and buttocks. OBJECTIVES: The aim of our study was to describe the assessment of the normal FTL and epimysium of the AM in MRI and to identify patterns associated with pathological changes in the lumbar spine. MATERIAL AND METHODS: A total of 33 patients were retrospectively evaluated: 15 patients had no pathology at the lumbar spine; six patients had previous hemilaminectomy, three had spondylodesis, two had ventrolisthesis, and seven had scoliosis. The thickness of the FTL and EM was measured, and the adhesion of both structures was assessed. RESULTS: The fascial thickness at the levels of the lumbar vertebral bodies LVB 3 was 1.8, of LVB 4 it was 2.0, of LVB 5 it was 2.1, and at the sacral vertebra SVB 1 it was 1.8 mm. Fascial adhesions together with thickening of the EM occurred at the level of LVB 4 in 36% of the cases independently of the underlying disorder. Only thickening of the EM was seen in 48% of cases at the level of SVB 1. By contrast, adhesion of the FTL without epimysial changes occurred in 36% of cases at the level of LVB 3. CONCLUSION: Thickening and adhesions at the EM and FTL occurred both postoperatively and in the case of scoliosis. Furthermore, lipomatous and muscular herniation could be detected in the FTL postoperatively. Epimysial and fascial alterations may be imaging manifestations of chronic myofascial back pain and should be included in radiological assessments.

Hierarchical Superstructures by Combining Crystallization-Driven and Molecular Self-Assembly.

Combining the unique corona structure of worm-like patchy micelles immobilized on a polymer fiber with the molecular self-assembly of 1,3,5-benzenetricarboxamides (BTAs) leads to hierarchical superstructures with a fir-tree-like morphology. For this purpose, worm-like patchy micelles bearing pendant, functional tertiary amino groups in one of the corona patches were prepared by crystallization-driven self-assembly and immobilized on a supporting polystyrene fiber by coaxial electrospinning. The obtained patchy fibers were then immersed in an aqueous solution of a tertiary amino-functionalized BTA to induce patch-mediated molecular self-assembly to well-defined fir-tree-like superstructures upon solvent evaporation. Interestingly, defined superstructures are obtained only if the pendant functional groups in the surface patches match with the peripheral substituents of the BTA, which is attributed to a local increase in BTA concentration at the polymer fibers' surface.

Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis.

The lipopolysaccharide biosynthesis pathway is considered an attractive drug target against the rising threat of multi-drug-resistant Gram-negative bacteria. Here, we report two novel small-molecule inhibitors (compounds 1 and 2) of the acyltransferase LpxA, the first enzyme in the lipopolysaccharide biosynthesis pathway. We show genetically that the antibacterial activities of the compounds against efflux-deficient Escherichia coli are mediated by LpxA inhibition. Consistently, the compounds inhibited the LpxA enzymatic reaction in vitro. Intriguingly, using biochemical, biophysical, and structural characterization, we reveal two distinct mechanisms of LpxA inhibition; compound 1 is a substrate-competitive inhibitor targeting apo LpxA, and compound 2 is an uncompetitive inhibitor targeting the LpxA/product complex. Compound 2 exhibited more favorable biological and physicochemical properties than compound 1 and was optimized using structural information to achieve improved antibacterial activity against wild-type E. coli. These results show that LpxA is a promising antibacterial target and imply the advantages of targeting enzyme/product complexes in drug discovery.

First Crystal Structure of a Nonstructural Hepatitis E Viral Protein Identifies a Putative Novel Zinc-Binding Protein.

Hepatitis E virus (HEV) is a 7.2-kb positive-sense, single-stranded RNA virus containing three partially overlapping reading frames, ORF1 to ORF3. All nonstructural proteins required for viral replication are encoded by ORF1 and are transcribed as a single transcript. Computational analysis of the complete ORF1 polyprotein identified a previously uncharacterized region of predicted secondary structure bordered by two disordered regions coinciding partially with a region predicted as a putative cysteine protease. Following successful cloning, expression, and purification of this region, the crystal structure of the identified protein was determined and identified to have considerable structural homology to a fatty acid binding domain. Further analysis of the structure revealed a metal binding site, shown unambiguously to specifically bind zinc via a nonclassical, potentially catalytic zinc-binding motif. Based on the structural homology of the HEV protein with known structures, along with the presence of a catalytic zinc-binding motif, it is possible that the identified protein corresponds to the HEV protease, which could require activation or repression through the binding of a fatty acid. This represents a significant step forward in the characterization and the understanding of the molecular mechanisms of the HEV genome. We present analysis for the first time of this identified nonstructural protein, expanding the knowledge and understanding of the complex mechanisms of HEV biology.IMPORTANCE Hepatitis E virus (HEV) is an emerging virus found predominately in developing countries; it causes an estimated 20 million infections, which result in approximately 57,000 deaths a year. Although it is known that the nonstructural proteins of HEV ORF1 are expressed as a single transcript, there is debate as to whether ORF1 functions as a single polyprotein or if it is processed into separate domains via a viral or endogenous cellular protease. Here we present the first structural and biophysical characterization of an HEV nonstructural protein using a construct that has partially overlapping boundaries with the predicted putative cysteine protease.

Supramolecular microtubes based on 1,3,5-benzenetricarboxamides prepared by self-assembly upon heating.

A series of three 1,3,5-benzenetricarboxamides with peripheral tertiary N,N-dialkyl-ethylamino substituents with different length of the alkyl groups is reported. In particular, the N1,N3,N5-tris[2-(diethylamino)-ethyl]-1,3,5-benzenetricarboxamide exhibits phase separation followed by self-assembly upon heating from aqueous solution into well-defined supramolecular fiber-like structures in the form of microtubes.

Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F†NMR-Based Screening.

Fragment-based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease-relevant targets. Among the numerous screening techniques, fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high-quality and diverse library containing nearly 4000 fragments and screening for target-specific binders within days. At the core of the approach is a novel broadband relaxation-edited NMR experiment that covers the entire chemical shift range of drug-like 19 F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.

Facilitating unambiguous NMR assignments and enabling higher probe density through selective labeling of all methyl containing amino acids.

The deuteration of proteins and selective labeling of side chain methyl groups has greatly enhanced the molecular weight range of proteins and protein complexes which can be studied using solution NMR spectroscopy. Protocols for the selective labeling of all six methyl group containing amino acids individually are available, however to date, only a maximum of five amino acids have been labeled simultaneously. Here, we describe a new methodology for the simultaneous, selective labeling of all six methyl containing amino acids using the 115 kDa homohexameric enzyme CoaD from E. coli as a model system. The utility of the labeling protocol is demonstrated by efficiently and unambiguously assigning all methyl groups in the enzymatic active site using a single 4D (13)C-resolved HMQC-NOESY-HMQC experiment, in conjunction with a crystal structure. Furthermore, the six fold labeled protein was employed to characterize the interaction between the substrate analogue (R)-pantetheine and CoaD by chemical shift perturbations, demonstrating the benefit of the increased probe density.

cis-Peptide Bonds: A Key for Intestinal Permeability of Peptides? .

Recent structural studies on libraries of cyclic hexapeptides led to the identification of common backbone conformations that may be instrumental to the oral availability of peptides. Furthermore, the observation of differential Caco-2 permeabilities of enantiomeric pairs of some of these peptides strongly supports the concept of conformational specificity driven uptake and also suggests a pivotal role of carrier-mediated pathways for peptide transport, especially for scaffolds of polar nature. This work presents investigations on the Caco-2 and PAMPA permeability profiles of 13 selected N-methylated cyclic pentaalanine peptides derived from the basic cyclo(-D-Ala-Ala4 -) template. These molecules generally showed moderate to low transport in intestinal epithelia with a few of them exhibiting a Caco-2 permeability equal to or slightly higher than that of mannitol, a marker for paracellular permeability. We identified that the majority of the permeable cyclic penta- and hexapeptides possess an N-methylated cis-peptide bond, a structural feature that is also present in the orally available peptides cyclosporine A and the tri-N-methylated analogue of the Veber-Hirschmann peptide. Based on these observations it appears that the presence of N-methylated cis-peptide bonds at certain locations may promote the intestinal permeability of peptides through a suitable conformational preorganization.

Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations.

Residual dipolar couplings are highly useful NMR parameters for calculating and refining molecular structures, dynamics, and interactions. For some applications, however, it is inevitable that the preferred orientation of a molecule in an alignment medium is calculated a priori. Several methods have been developed to predict molecular orientations and residual dipolar couplings. Being beneficial for macromolecules and selected small-molecule applications, such approaches lack sufficient accuracy for a large number of organic compounds for which the fine structure and eventually the flexibility of all involved molecules have to be considered or are limited to specific, well-studied liquid crystals. We introduce a simplified model for detailed all-atom molecular dynamics calculations with a polymer strand lined up along the principal axis as a new approach to simulate the preferred orientation of small to medium-sized solutes in polymer-based, gel-type alignment media. As is shown by a first example of strychnine in a polystyrene/CDCl3 gel, the simulations potentially enable the accurate prediction of residual dipolar couplings taking into account structural details and dynamic averaging effects of both the polymer and the solute.

Receptor-bound conformation of cilengitide better represented by its solution-state structure than the solid-state structure.

The X-ray crystal and NMR spectroscopic structures of the peptide drug candidate Cilengitide (cyclo(RGDf(NMe)Val)) in various solvents are obtained and compared in addition to the integrin receptor bound conformation. The NMR-based solution structures exhibit conformations closely resembling the X-ray structure of Cilengitide bound to the head group of integrin αvß3. In contrast, the structure of pure Cilengitide recrystallized from methanol reveals a different conformation controlled by the lattice forces of the crystal packing. Molecular modeling studies of the various ligand structures docked to the αvß3 integrin revealed that utilization of the solid-state conformation of Cilengitide leads-unlike the solution-based structures-to a mismatch of the ligand-receptor interactions compared with the experimentally determined structure of the protein-ligand complex. Such discrepancies between solution and crystal conformations of ligands can be misleading during the structure-based lead optimization process and should thus be taken carefully into account in ligand orientated drug design.

Surface reengineering of RPA70N enables cocrystallization with an inhibitor of the replication protein A interaction motif of ATR interacting protein.

Replication protein A (RPA) is the primary single-stranded DNA (ssDNA) binding protein in eukaryotes. The N-terminal domain of the RPA70 subunit (RPA70N) interacts via a basic cleft with a wide range of DNA processing proteins, including several that regulate DNA damage response and repair. Small molecule inhibitors that disrupt these protein-protein interactions are therefore of interest as chemical probes of these critical DNA processing pathways and as inhibitors to counter the upregulation of DNA damage response and repair associated with treatment of cancer patients with radiation or DNA-damaging agents. Determination of three-dimensional structures of protein-ligand complexes is an important step for elaboration of small molecule inhibitors. However, although crystal structures of free RPA70N and an RPA70N-peptide fusion construct have been reported, RPA70N-inhibitor complexes have been recalcitrant to crystallization. Analysis of the P61 lattice of RPA70N crystals led us to hypothesize that the ligand-binding surface was occluded. Surface reengineering to alter key crystal lattice contacts led to the design of RPA70N E7R, E100R, and E7R/E100R mutants. These mutants crystallized in a P212121 lattice that clearly had significant solvent channels open to the critical basic cleft. Analysis of X-ray crystal structures, target peptide binding affinities, and (15)N-(1)H heteronuclear single-quantum coherence nuclear magnetic resonance spectra showed that the mutations do not result in perturbations of the RPA70N ligand-binding surface. The success of the design was demonstrated by determining the structure of RPA70N E7R soaked with a ligand discovered in a previously reported molecular fragment screen. A fluorescence anisotropy competition binding assay revealed this compound can inhibit the interaction of RPA70N with the peptide binding motif from the DNA damage response protein ATRIP. The implications of the results are discussed in the context of ongoing efforts to design RPA70N inhibitors.