Chemical Catalysis Guides Structural Identification for the Major In Vivo Metabolite of the BET Inhibitor JQ1.

The bromodomain inhibitor (+)-JQ1 is a highly validated chemical probe; however, it exhibits poor in vivo pharmacokinetics. To guide efforts toward improving its pharmacological properties, we identified the (+)-JQ1 primary metabolite using chemical catalysis methods. Treatment of (+)-JQ1 with tetrabutylammonium decatungstate under photochemical conditions resulted in selective formation of an aldehyde at the 2-position of the thiophene ring [(+)-JQ1-CHO], which was further reduced to the 2-hydroxymethyl analog [(+)-JQ1-OH]. Comparative LC/MS analysis of (+)-JQ1-OH to the product obtained from liver microsomes suggested (+)-JQ1-OH as the major metabolite of (+)-JQ1. The 2-thienyl position was then substituted to generate a trideuterated (-CD3, (+)-JQ1-D) analog having half-lives that were 1.8- and 2.8-fold longer in mouse and human liver microsomes, respectively. This result unambiguously confirmed (+)-JQ1-OH as the major metabolite of (+)-JQ1. These studies demonstrate an efficient process for studying drug metabolism and identifying the metabolic soft spots of bioactive compounds.

Processing binding data using an open-source workflow.

The thermal shift assay (TSA)-also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift-is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein-ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There are several approaches that aim to streamline this process, but most involve proprietary software, programming knowledge, or are designed for specific instrument output files. We therefore developed an analysis workflow implemented in the Konstanz Information Miner (KNIME), a free and open-source data analytics platform, which greatly streamlined our data processing timeline for 384-well plates. The implementation is code-free and freely available to the community for improvement and customization to accommodate a wide range of instrument input files and workflows.

Design and construction of a stereochemically diverse piperazine-based DNA-encoded chemical library.

Here we report the successful construction of a novel, stereochemically diverse DNA-Encoded Chemical Library (DECL) by utilizing 24 enantiomerically pure trifunctional 2, 6- di-substituted piperazines as central cores. We introduce the concept of positional diversity by placing the DNA attachment at either of two possible sites on the piperazine scaffold. Using a wide range of building blocks, a diverse library of 77 million compounds was produced. Cheminformatic analysis demonstrates that this library occupies a wide swath of chemical space, and that the piperazine scaffolds confers different shape diversity compared to the commonly used triazine core.

Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery.

Despite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, we use fragment-based ligand discovery to identify novel scaffolds for targeting the isolated UHRF1 tandem Tudor domain (TTD), which recognizes the heterochromatin-associated histone mark H3K9me3 and supports intramolecular contacts with other regions of UHRF1. Using both binding-based and function-based screens of a ~ 2300-fragment library in parallel, we identified 2,4-lutidine as a hit for follow-up NMR and X-ray crystallography studies. Unlike previous reported ligands, 2,4-lutidine binds to two binding pockets that are in close proximity on TTD and so has the potential to be evolved into more potent inhibitors using a fragment-linking strategy. Our study provides a useful starting point for developing potent chemical probes against UHRF1.

Enteral Activation of WR-2721 Mediates Radioprotection and Improved Survival from Lethal Fractionated Radiation.

Unresectable pancreatic cancer is almost universally lethal because chemotherapy and radiation cannot completely stop the growth of the cancer. The major problem with using radiation to approximate surgery in unresectable disease is that the radiation dose required to ablate pancreatic cancer exceeds the tolerance of the nearby duodenum. WR-2721, also known as amifostine, is a well-known radioprotector, but has significant clinical toxicities when given systemically. WR-2721 is a prodrug and is converted to its active metabolite, WR-1065, by alkaline phosphatases in normal tissues. The small intestine is highly enriched in these activating enzymes, and thus we reasoned that oral administration of WR-2721 just before radiation would result in localized production of the radioprotective WR-1065 in the small intestine, providing protective benefits without the significant systemic side effects. Here, we show that oral WR-2721 is as effective as intraperitoneal WR-2721 in promoting survival of intestinal crypt clonogens after morbid irradiation. Furthermore, oral WR-2721 confers full radioprotection and survival after lethal upper abdominal irradiation of 12.5 Gy × 5 fractions (total of 62.5 Gy, EQD2 = 140.6 Gy). This radioprotection enables ablative radiation therapy in a mouse model of pancreatic cancer and nearly triples the median survival compared to controls. We find that the efficacy of oral WR-2721 stems from its selective accumulation in the intestine, but not in tumors or other normal tissues, as determined by in vivo mass spectrometry analysis. Thus, we demonstrate that oral WR-2721 is a well-tolerated, and quantitatively selective, radioprotector of the intestinal tract that is capable of enabling clinically relevant ablative doses of radiation to the upper abdomen without unacceptable gastrointestinal toxicity.

Preferential uptake of antioxidant carbon nanoparticles by T lymphocytes for immunomodulation.

Autoimmune diseases mediated by a type of white blood cell-T lymphocytes-are currently treated using mainly broad-spectrum immunosuppressants that can lead to adverse side effects. Antioxidants represent an alternative approach for therapy of autoimmune disorders; however, dietary antioxidants are insufficient to play this role. Antioxidant carbon nanoparticles scavenge reactive oxygen species (ROS) with higher efficacy than dietary and endogenous antioxidants. Furthermore, the affinity of carbon nanoparticles for specific cell types represents an emerging tactic for cell-targeted therapy. Here, we report that nontoxic poly(ethylene glycol)-functionalized hydrophilic carbon clusters (PEG-HCCs), known scavengers of the ROS superoxide (O2•-) and hydroxyl radical, are preferentially internalized by T lymphocytes over other splenic immune cells. We use this selectivity to inhibit T cell activation without affecting major functions of macrophages, antigen-presenting cells that are crucial for T cell activation. We also demonstrate the in vivo effectiveness of PEG-HCCs in reducing T lymphocyte-mediated inflammation in delayed-type hypersensitivity and in experimental autoimmune encephalomyelitis, an animal model of multiple sclerosis. Our results suggest the preferential targeting of PEG-HCCs to T lymphocytes as a novel approach for T lymphocyte immunomodulation in autoimmune diseases without affecting other immune cells.

Biocompatibility of reduced graphene oxide nanoscaffolds following acute spinal cord injury in rats.

BACKGROUND: Graphene has unique electrical, physical, and chemical properties that may have great potential as a bioscaffold for neuronal regeneration after spinal cord injury. These nanoscaffolds have previously been shown to be biocompatible in vitro; in the present study, we wished to evaluate its biocompatibility in an in vivo spinal cord injury model. METHODS: Graphene nanoscaffolds were prepared by the mild chemical reduction of graphene oxide. Twenty Wistar rats (19 male and 1 female) underwent hemispinal cord transection at approximately the T2 level. To bridge the lesion, graphene nanoscaffolds with a hydrogel were implanted immediately after spinal cord transection. Control animals were treated with hydrogel matrix alone. Histologic evaluation was performed 3 months after the spinal cord transection to assess in vivo biocompatibility of graphene and to measure the ingrowth of tissue elements adjacent to the graphene nanoscaffold. RESULTS: The graphene nanoscaffolds adhered well to the spinal cord tissue. There was no area of pseudocyst around the scaffolds suggestive of cytotoxicity. Instead, histological evaluation showed an ingrowth of connective tissue elements, blood vessels, neurofilaments, and Schwann cells around the graphene nanoscaffolds. CONCLUSIONS: Graphene is a nanomaterial that is biocompatible with neurons and may have significant biomedical application. It may provide a scaffold for the ingrowth of regenerating axons after spinal cord injury.

Characterization of a novel MR-detectable nanoantioxidant that mitigates the recall immune response.

In many human diseases, the presence of inflammation is associated with an increase in the level of reactive oxygen species (ROS). The resulting state of oxidative stress is highly detrimental and can initiate a cascade of events that ultimately lead to cell death. Thus, many therapeutic attempts have been focused on either modulating the immune system to lower inflammation or reducing the damaging caused by ROS. Berlin et al. reported the development of a novel nanoantioxidant known as poly(ethylene glycol)-functionalized-hydrophilic carbon clusters (PEG-HCCs). They showed that PEG-HCCs could be targeted to cancer cells, utilized as a drug delivery vector, and can even be visualized ex vivo. Our work here furthers this work and characterizes Gd-DTPA conjugated PEG-HCCs and explores the potential for in vivo tracking of T cells in live mice. We utilized a mouse model of delayed-type hypersensitivity (DTH) to assess the immunomodulatory effects of PEG-HCCs. The T1 -agent Gd-DTPA was then conjugated to the PEG-HCCs and T1 measurements, and T1 -weighted MRI of the modified PEG-HCCs was done to assess their relaxivity. We then assessed if PEG-HCCs could be visualized both ex vivo and in vivo within the mouse lymph node and spleen. Mice treated with PEG-HCCs showed significant improvements in the DTH assay as compared to the vehicle (saline)-treated control. Flow cytometry demonstrated that splenic T cells are capable of internalizing PEG-HCCs whereas fluorescent immunohistochemistry showed that PEG-HCCs are detectable within the cortex of lymph nodes. Finally, our nanoantioxidants can be visualized in vivo within the lymph nodes and spleen of a mouse after addition of the Gd-DTPA. PEG-HCCs are internalized by T cells in the spleen and can reduce inflammation by suppression of a recall immune response. PEG-HCCs can be modified to allow for both in vitro and in vivo visualization using MRI. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

Mechanistic Study of the Conversion of Superoxide to Oxygen and Hydrogen Peroxide in Carbon Nanoparticles.

Hydrophilic carbon clusters (HCCs) are oxidized carbon nanoparticles with a high affinity for electrons. The electron accepting strength of HCCs, employing the efficient conversion of superoxide (O2(•-)) to molecular oxygen (O2) via single-electron oxidation, was monitored using cyclic voltammetry and electron paramagnetic resonance spectroscopy. We found that HCCs possess O2 reduction reaction (ORR) capabilities through a two-electron process with the formation of H2O2. By comparing results from aprotic solvents to those obtained from ORR activity in aqueous media, we propose a mechanism for the origin of the antioxidant and superoxide dismutase mimetic properties of poly(ethylene glycolated) hydrophilic carbon clusters (PEG-HCCs).

Atomic cobalt on nitrogen-doped graphene for hydrogen generation.

Reduction of water to hydrogen through electrocatalysis holds great promise for clean energy, but its large-scale application relies on the development of inexpensive and efficient catalysts to replace precious platinum catalysts. Here we report an electrocatalyst for hydrogen generation based on very small amounts of cobalt dispersed as individual atoms on nitrogen-doped graphene. This catalyst is robust and highly active in aqueous media with very low overpotentials (30 mV). A variety of analytical techniques and electrochemical measurements suggest that the catalytically active sites are associated with the metal centres coordinated to nitrogen. This unusual atomic constitution of supported metals is suggestive of a new approach to preparing extremely efficient single-atom catalysts.

The microRNA miR-22 inhibits the histone deacetylase HDAC4 to promote T(H)17 cell-dependent emphysema.

Smoking-related emphysema is a chronic inflammatory disease driven by the T(H)17 subset of helper T cells through molecular mechanisms that remain obscure. Here we explored the role of the microRNA miR-22 in emphysema. We found that miR-22 was upregulated in lung myeloid dendritic cells (mDCs) of smokers with emphysema and antigen-presenting cells (APCs) of mice exposed to smoke or nanoparticulate carbon black (nCB) through a mechanism that involved the transcription factor NF-κB. Mice deficient in miR-22, but not wild-type mice, showed attenuated T(H)17 responses and failed to develop emphysema after exposure to smoke or nCB. We further found that miR-22 controlled the activation of APCs and T(H)17 responses through the activation of AP-1 transcription factor complexes and the histone deacetylase HDAC4. Thus, miR-22 is a critical regulator of both emphysema and T(H)17 responses.

Cobalt nanoparticles embedded in nitrogen-doped carbon for the hydrogen evolution reaction.

There is great interest in renewable and sustainable energy research to develop low-cost, highly efficient, and stable electrocatalysts as alternatives to replace Pt-based catalysts for the hydrogen evolution reaction (HER). Though nanoparticles encapsulated in carbon shells have been widely used to improve the electrode performances in energy storage devices (e.g., lithium ion batteries), they have attracted less attention in energy-related electrocatalysis. Here we report the synthesis of nitrogen-enriched core-shell structured cobalt-carbon nanoparticles dispersed on graphene sheets and we investigate their HER performances in both acidic and basic media. These catalysts exhibit excellent durability and HER activities with onset overpotentials as low as ∼70 mV in both acidic (0.5 M H2SO4) and alkaline (0.1 M NaOH) electrolytes, and the overpotentials needed to deliver 10 mA cm(-2) are determined to be 265 mV in acid and 337 mV in base, further demonstrating their potential to replace Pt-based catalysts. Control experiments reveal that the active sites for HER might come from the synergistic effects between the cobalt nanoparticles and nitrogen-doped carbon.

Bandgap engineering of coal-derived graphene quantum dots.

Bandgaps of photoluminescent graphene quantum dots (GQDs) synthesized from anthracite have been engineered by controlling the size of GQDs in two ways: either chemical oxidative treatment and separation by cross-flow ultrafiltration, or by a facile one-step chemical synthesis using successively higher temperatures to render smaller GQDs. Using these methods, GQDs were synthesized with tailored sizes and bandgaps. The GQDs emit light from blue-green (2.9 eV) to orange-red (2.05 eV), depending on size, functionalities and defects. These findings provide a deeper insight into the nature of coal-derived GQDs and demonstrate a scalable method for production of GQDs with the desired bandgaps.

Highly efficient conversion of superoxide to oxygen using hydrophilic carbon clusters.

Many diseases are associated with oxidative stress, which occurs when the production of reactive oxygen species (ROS) overwhelms the scavenging ability of an organism. Here, we evaluated the carbon nanoparticle antioxidant properties of poly(ethylene glycolated) hydrophilic carbon clusters (PEG-HCCs) by electron paramagnetic resonance (EPR) spectroscopy, oxygen electrode, and spectrophotometric assays. These carbon nanoparticles have 1 equivalent of stable radical and showed superoxide (O2 (•-)) dismutase-like properties yet were inert to nitric oxide (NO(•)) as well as peroxynitrite (ONOO(-)). Thus, PEG-HCCs can act as selective antioxidants that do not require regeneration by enzymes. Our steady-state kinetic assay using KO2 and direct freeze-trap EPR to follow its decay removed the rate-limiting substrate provision, thus enabling determination of the remarkable intrinsic turnover numbers of O2 (•-) to O2 by PEG-HCCs at >20,000 s(-1). The major products of this catalytic turnover are O2 and H2O2, making the PEG-HCCs a biomimetic superoxide dismutase.

Flexible and stackable laser-induced graphene supercapacitors.

In this paper, we demonstrate that by simple laser induction, commercial polyimide films can be readily transformed into porous graphene for the fabrication of flexible, solid-state supercapacitors. Two different solid-state electrolyte supercapacitors are described, namely vertically stacked graphene supercapacitors and in-plane graphene microsupercapacitors, each with enhanced electrochemical performance, cyclability, and flexibility. Devices with a solid-state polymeric electrolyte exhibit areal capacitance of >9 mF/cm2 at a current density of 0.02 mA/cm2, more than twice that of conventional aqueous electrolytes. Moreover, laser induction on both sides of polyimide sheets enables the fabrication of vertically stacked supercapacitors to multiply its electrochemical performance while preserving device flexibility.

Asphalt-derived high surface area activated porous carbons for carbon dioxide capture.

Research activity toward the development of new sorbents for carbon dioxide (CO2) capture have been increasing quickly. Despite the variety of existing materials with high surface areas and high CO2 uptake performances, the cost of the materials remains a dominant factor in slowing their industrial applications. Here we report preparation and CO2 uptake performance of microporous carbon materials synthesized from asphalt, a very inexpensive carbon source. Carbonization of asphalt with potassium hydroxide (KOH) at high temperatures (>600 °C) yields porous carbon materials (A-PC) with high surface areas of up to 2780 m(2) g(-1) and high CO2 uptake performance of 21 mmol g(-1) or 93 wt % at 30 bar and 25 °C. Furthermore, nitrogen doping and reduction with hydrogen yields active N-doped materials (A-NPC and A-rNPC) containing up to 9.3% nitrogen, making them nucleophilic porous carbons with further increase in the Brunauer-Emmett-Teller (BET) surface areas up to 2860 m(2) g(-1) for A-NPC and CO2 uptake to 26 mmol g(-1) or 114 wt % at 30 bar and 25 °C for A-rNPC. This is the highest reported CO2 uptake among the family of the activated porous carbonaceous materials. Thus, the porous carbon materials from asphalt have excellent properties for reversibly capturing CO2 at the well-head during the extraction of natural gas, a naturally occurring high pressure source of CO2. Through a pressure swing sorption process, when the asphalt-derived material is returned to 1 bar, the CO2 is released, thereby rendering a reversible capture medium that is highly efficient yet very inexpensive.

Laser-induced porous graphene films from commercial polymers.

The cost effective synthesis and patterning of carbon nanomaterials is a challenge in electronic and energy storage devices. Here we report a one-step, scalable approach for producing and patterning porous graphene films with three-dimensional networks from commercial polymer films using a CO2 infrared laser. The sp3-carbon atoms are photothermally converted to sp2-carbon atoms by pulsed laser irradiation. The resulting laser-induced graphene (LIG) exhibits high electrical conductivity. The LIG can be readily patterned to interdigitated electrodes for in-plane microsupercapacitors with specific capacitances of >4 mF cm-2 and power densities of ~9 mW cm-2. Theoretical calculations partially suggest that enhanced capacitance may result from LIG's unusual ultra-polycrystalline lattice of pentagon-heptagon structures. Combined with the advantage of one-step processing of LIG in air from commercial polymer sheets, which would allow the employment of a roll-to-roll manufacturing process, this technique provides a rapid route to polymer-written electronic and energy storage devices.

Functionalized graphene nanoribbon films as a radiofrequency and optically transparent material.

We report that conductive films made from hexadecylated graphene nanoribbons (HD-GNRs) can have high transparency to radiofrequency (RF) waves even at very high incident power density. Nanoscale-thick HD-GNR films with an area of several square centimeters were found to transmit up to 390 W (2 × 10(5) W/m(2)) of RF power with negligible loss, at an RF transmittance of ∼99%. The HD-GNR films conformed to electromagnetic skin depth theory, which effectively accounts for the RF transmission. The HD-GNR films also exhibited sufficient optical transparency for tinted glass applications, with efficient voltage-induced deicing of surfaces. The dispersion of the HD-GNRs afforded by their edge functionalization enables spray-, spin-, or blade-coating on almost any substrate, thus facilitating flexible, conformal, and large-scale film production. In addition to use in antennas and radomes where RF transparency is crucial, these capabilities bode well for the use of the HD-GNR films in automotive and general glass applications where both optical and RF transparencies are desired.

Hydrophilic carbon clusters as therapeutic, high-capacity antioxidants.

Oxidative stress reflects an excessive accumulation of reactive oxygen species (ROS) and is a hallmark of several acute and chronic human pathologies. Although many antioxidants have been investigated, most have demonstrated poor efficacy in clinical trials. Here we discuss the limitations of current antioxidants and describe a new class of nanoparticle antioxidants, poly(ethylene glycol)-functionalized hydrophilic carbon clusters (PEG-HCCs). PEG-HCCs show high capacity to annihilate ROS such as superoxide (O2(•-)) and the hydroxyl (HO(•)) radical, show no reactivity toward the nitric oxide radical (NO(•)), and can be functionalized with targeting moieties without loss of activity. Given these properties, we propose that PEG-HCCs offer an exciting new area of study for the treatment of numerous ROS-induced human pathologies.