Search

USP5 is a deubiquitinase that has been implicated in a range of diseases, including cancer, but no USP5-targeting chemical probe has been reported to date. Here, we present the progression of a chemical series that occupies the C-terminal ubiquitin-binding site of a poorly characterized zinc-finger ubiquitin binding domain (ZnF-UBD) of USP5 and competitively inhibits the catalytic activity of the enzyme. Exploration of the structure-activity relationship, complemented with crystallographic characterization of the ZnF-UBD bound to multiple ligands, led to the identification of 64, which binds to the USP5 ZnF-UBD with a KD of 2.8 μM and is selective over nine proteins containing structurally similar ZnF-UBD domains. 64 inhibits the USP5 catalytic cleavage of a di-ubiquitin substrate in an in vitro assay. This study provides a chemical and structural framework for the discovery of a chemical probe to delineate USP5 function in cells.

USP5 is a deubiquitinase that has been implicated in a range of diseases, including cancer, but no USP5-targeting chemical probe has been reported to date. Here, we present the progression of a chemical series that occupies the C-terminal ubiquitin-binding site of a poorly characterized zinc-finger ubiquitin binding domain (ZnF-UBD) of USP5 and allosterically inhibits the catalytic activity of the enzyme. Systematic exploration of the structure-activity relationship, complemented with crystallographic characterization of the ZnF-UBD bound to multiple ligands, led to the identification of 64, which binds to the USP5 ZnF-UBD with a KD of 2.8 µM. 64 is selective over the structurally similar ZnF-UBD domain of HDAC6 and inhibits USP5 catalytic activity in vitro with an IC50 of 26 µM. This study provides a chemical and structural framework for the discovery of a chemical probe to delineate USP5 function in cells. Table of Contents Graphic

USP5 disassembles unanchored polyubiquitin chains to recycle free monoubiquitin, and is one of the 12 ubiquitin specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship, which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signaling pathways in health and disease.

USP5 disassembles unanchored polyubiquitin chains to recycle free mono-ubiquitin, and is one of twelve ubiquitin-specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signalling pathways in health and disease.

HDAC6 plays a central role in the recruitment of protein aggregates for lysosomal degradation, and is a promising target for combination therapy with proteasome inhibitors in multiple myeloma. Pharmacologically displacing ubiquitin from the zinc-finger ubiquitin-binding domain (ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition. Here, we present the discovery of a HDAC6 ZnF-UBD-focused chemical series and its progression from virtual screening hits to low micromolar inhibitors. A carboxylate mimicking the C-terminal extremity of ubiquitin, and an extended aromatic system stacking with W1182 and R1155 are necessary for activity. One of the compounds induced a conformational remodeling of the binding site where the primary binding pocket opens-up onto a ligand-able secondary pocket that may be exploited to increase potency. The preliminary structure-activity relationship accompanied by nine crystal structures should enable further optimization into a chemical probe to investigate the merit of targeting the ZnF-UBD of HDAC6 in multiple myeloma and other diseases.

The generation of electricity, and the consumption of energy in general, often result in adverse effects on the environment. Coal-fired power plants generate over half of the electricity used in the U.S., and therefore play a significant role in any discussion of energy and the environment. By cofiring biomass, currently operating coal plants have an opportunity to reduce the impact they have, but to what degree, and with what trade-offs? A life cycle assessment has been conducted on a coal-fired power system that cofires wood residue. The assessment was conducted in a cradle-to-grave manner to cover all processes necessary for the operation of the power plant, including raw material extraction, feed preparation, transportation, and waste disposal and recycling. Cofiring was found to significantly reduce the environmental footprint of the average coal-fired power plant. At rates of 5% and 15% by heat input, cofiring reduces greenhouse gas emissions on a CO2-equivalent basis by 5.4% and 18.2%, respectively. Emissions of SO2, NOx, non-methane hydrocarbons, particulates, and carbon monoxide are also reduced with cofiring. Additionally, total system energy consumption is lowered by 3.5% and 12.4% for the 5% and 15% cofiring cases, respectively. Finally, resource consumption and solid waste generation were found to be much less for systems that cofire.

The technical and economic feasibility of producing hydrogen from biomass by means of indirectly heated gasification and steam reforming was studied. A detailed process model was developed in ASPEN Plus{trademark} to perform material and energy balances. The results of this simulation were used to size and cost major pieces of equipment from which the determination of the necessary selling price of hydrogen was made. A sensitivity analysis was conducted on the process to study hydrogen price as a function of biomass feedstock cost and hydrogen production efficiency. The gasification system used for this study was the Battelle Columbus Laboratory (BCL) indirectly heated gasifier. The heat necessary for the endothermic gasification reactions is supplied by circulating sand from a char combustor to the gasification vessel. Hydrogen production was accomplished by steam reforming the product synthesis gas (syngas) in a process based on that used for natural gas reforming. Three process configurations were studied. Scheme 1 is the full reforming process, with a primary reformer similar to a process furnace, followed by a high temperature shift reactor and a low temperature shift reactor. Scheme 2 uses only the primary reformer, and Scheme 3 uses the primary reformer and the high temperature shift reactor. A pressure swing adsorption (PSA) system is used in all three schemes to produce a hydrogen product pure enough to be used in fuel cells. Steam is produced through detailed heat integration and is intended to be sold as a by-product.

The general architecture of the US National Airspace System (NAS) is presented. Background on the overall air traffic control (ATC) system's history is given as prologue to descriptions of the major elements of the NAS Plan, the US Federal Aviation Administration's current effort to upgrade and modernize the ATC system. Technologies central to achieving the planned end-state configuration for each element are characterized in terms of their functional impact and potential benefit. Communications, navigation aids, weather support, surveillance, and maintenance systems are all undergoing significant technology upgrade. Digital processing capabilities and communications technology lead the way in permitting this modernization program to become reality. Significant consolidation efforts are yielding a much more cost-effective, responsive, and flexible ATC environment. >