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DOE OSTI2022

Research and Test Reactor Fuels

PRO-RR is the research reactor focused program element of the broader Proliferation Resistance Optimization program (PRO-X) under the National Nuclear Safety Administration (NNSA) in the U.S. Department of Energy (DOE). PRO-X provides a framework for integrating proliferation resistance in nuclear system designs to minimize weapons usable nuclear materials (WUNM) production and diversion pathways while optimizing systems performance for peaceful use missions. PRO-RR applies the PRO-X mission objectives to research reactor system design. This document serves as one of the foundational documents for the PRO-RR-Fuel System Design technical team by documenting current research reactor fuels usage. The PRO-RR-Fuel System Design technical team consists of subject matter experts from Argonne National Laboratory (Argonne) and Savannah River National Laboratory (SRNL). In order to determine the preferred fuel of use in upcoming research and test reactors to optimize proliferation resistance, performance, and safety, it is useful to assess the fuels that have been used in the past, or are currently in use. This report reviews the historical and current fuels used in research and test reactors to inform future fuel selection. Chapter 2 discusses the low-enriched uranium (LEU) fuels currently in use in terms of thermal power level and utilization of the reactor. Chapter 3 summarizes the fabrication processes for common fuel types. Chapter 4 discusses in detail the fuel types in use in research and test reactors. A review of the cladding types in use is presented in Chapter 5, and a historical review of research and test reactor fuel fabricators is presented in Chapter 6. The data collection strategy used the International Atomic Energy Agency (IAEA) research reactor database [1] as a starting point. Information on the fuel used was gathered on research reactors (other than critical assemblies) that were listed as operational, planned, or in temporary shutdown in the IAEA database. Data on the fuel type, geometry, enrichment, uranium loading, cladding type, and fabricator were collected for each of the reactors available in the public domain. Sources of data included conference papers, journal articles, and facility and fabricator websites. Data on research reactors operating on LEU fuels are presented in Appendix A, while Appendix B presents data collected on all reactors at the time of publication of this report. Appendix C presents data collected on reactors that were part of the M3 research and test reactor conversion program.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

Baseline Fuel Fabrication Facility

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2020

A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors**

The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2M Pro ) to digest two of its translated long polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replicating in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1M Pro ), we have designed and synthesized a series of SC2M Pro inhibitors that contain β-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2M Pro active-site cysteine C145. All inhibitors display high potency with K i values at or below 100 nM. The most potent compound, MPI3, has as a K i value of 8.3 nM. Crystallographic analyses of SC2M Pro bound to seven inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549/ACE2 cells. Two inhibitors, MPI5 and MPI8, completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 μM and A549/ACE2 cells at 0.16-0.31 μM. Their virus inhibition potency is much higher than that of some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2M Pro inhibitors with ultra-high antiviral potency.

3C-like protease↗

DOE OSTI2023

The effects of protease, xylanase, and xylo-oligosaccharides on growth performance, nutrient utilization, short-chain fatty acids, and microbiota in Eimeria -challenged broiler chickens fed low-protein diet

A total of 392 Cobb 500 off-sex male broiler chicks were used in a 21-day experiment to study the effect of protease, xylanase, and xylo-oligosaccharides (XOS) on improving growth performance, nutrient utilization (ileal digestibility and total tract retention), gene expression of nutrient transporters, cecal short-chain fatty acids (SCFAs), and microbiota profile of broilers challenged with Eimeria spp. Chicks at 0-day old were allocated to 8 treatments in a 4 × 2 factorial arrangement: 1) corn-soybean meal diet with no enzyme (Con); 2) Con plus 0.2 g/kg protease alone (PRO); 3) Con plus 0.2 g/kg protease combined with 0.1 g/kg xylanase (PRO + XYL); or 4) Con plus 0.5 g/kg xylo-oligosaccharides (XOS); with or without Eimeria challenge. The 4 diets were formulated to be marginally low in crude protein (183 g/kg). Challenged groups were inoculated with a solution containing E. maxima, E. acervulina, and E. tenella oocysts on d 15. Eimeria depressed (P < 0.01) growth performance and nutrient utilization. Supplemental protease improved (P < 0.05) body weight gain and feed intake in the prechallenge phase (d 0-15) but had no effect during the infection period (d 15-21). There was no interaction between infection and feed supplementation for nutrient utilization. The supplementations of either PRO or XOS alone increased (P < 0.01) total tract retention of Ca and tended (P < 0.1) to improve total tract retention of N, P, AME, and AMEn. Eimeria decreased (P < 0.05) expressions of GLUT2, GLUT5, PepT1, ATP2B1, CaSR, Calbidin D28K, NPT2, and ZnT1 but increased (P < 0.01) expression of GLUT1. XOS supplementation increased (P < 0.05) ATP2B1 expression. Protease decreased (P < 0.05) isobutyrate concentration in unchallenged treatments but not in challenged treatments. Eimeria decreased (P < 0.01) cecal saccharolytic SCFAs acetate and propionate but increased (P < 0.01) branched-chain fatty acid isovalerate. The supplementation of PRO + XYL or XOS increased (P < 0.05) cecal butyrate or decreased cecal isobutyrate concentrations, respectively. PRO + XYL and XOS decreased cecal protein levels in unchallenged birds but not challenged ones. Eimeria challenge significantly (P < 0.05) decreased the microbial richness (Observed features) and diversity (Shannon index and phylogenetic diversity) and changed the microbial composition by reducing the abundance of certain bacteria, such as Ruminococcus torques, and increasing the abundance of others, such as Anaerostipes. In contrast, none of the additives had any significant effect on the cecal microbial composition. In conclusion, PRO or XOS supplementation individually improved nutrient utilization. All the additives decreased the cecal content of branched-chain fatty acids, consistent with decreased cecal N concentration, although the effects were more pronounced in unchallenged birds. In addition, none of the feed additives impacted the Eimeria-induced microbial perturbation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors

The development of SARS-CoV-2 main protease (M pro ) inhibitors for the treatment of COVID-19 has mostly benefitted from X-ray structures and preexisting knowledge of inhibitors; however, an efficient method to generate M pro inhibitors, which circumvents such information would be advantageous. As an alternative approach, we show here that DNA-encoded chemistry technology (DEC-Tec) can be used to discover inhibitors of M pro . An affinity selection of a 4-billion-membered DNA-encoded chemical library (DECL) using M pro as bait produces novel non-covalent and non-peptide-based small molecule inhibitors of M pro with low nanomolar K i values. Furthermore, these compounds demonstrate efficacy against mutant forms of M pro that have shown resistance to the standard-of-care drug nirmatrelvir. Overall, this work demonstrates that DEC-Tec can efficiently generate novel and potent inhibitors without preliminary chemical or structural information.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1998

Beta-Adrenergic Blockade Does not Prevent Polycythemia or Decrease in Plasma Volume in Men at 4300 m Altitude

When humans ascend to high altitude (ALT) their plasma volume (PV) and total blood volume (BV) decrease during the first few days. With continued residence over several weeks, the hypoxia-induced stimulation of erythropoietin increases red cell production which tends to restore BV. Because hypoxia also activates the beta-adrenergic system, which stimulates red blood cell production, we investigated the effect of adrenergic beta-receptor inhibition with propranolol on fluid volumes and the polycythemic response in 11 healthy unacclimatized men (21-33 years old exposed to an ALT of 4300 m (barometric pressure 460 Torr) for 3 weeks on Pikes Peak, Colorado. PV was determined by the Evans blue dye method (PV(sub EB)), BV by the carbon monoxide method (BV(sub CO)), red cell volume (RCV)was calculated from hematocrit (Hct) and BV(sub CO), and serum erythropoietin concentration ([EPO]) and reticulocyte count, were also determined. All determinations were made at sea level and after 9-11 (ALT-10) and 9-20 (ALT-20) days at ALT. At sea level and ALT, six men received propranolol (pro, 240 mg/day), and five received a placebo (pla). Effective beta-blockade did not modify the mean (SE) maximal values of [EPO] [pla: 24.9 (3.5) vs pro: 24.5 (1.5) mU/ml] or reticulocyte count [pla: 2.7 (0.7) vs pro: 2.2 (0.5)%]; nor changes in PV(sub EB)[pla: -15.8 (3.8) vs pro: -19.9 (2.8)%], RCV(sub CO) [pla: +7.0 (6.7) vs pro: +10.1 (6.1)%], or BV(sub CO) [pla: -7.3 (2.3) vs pro: -7.1 (3.9)%]. In the absence of weight loss, a redistribution of body water with no net loss is implied. Hence, activation of the beta-adrenergic system did not appear to affect the hypovolemic or polycythemic responses that occurred during 3 weeks at 4300 m ALT in these subjects.

Grover, R. F.↗

DOE OSTI2023

Development of the Safe and Broad‐Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained α, γ‐AA Peptide Scaffold

Abstract SARS‐CoV‐2 is still wreaking havoc all over the world with surging morbidity and high mortality. The main protease (M pro ) is essential in the replication of SARS‐CoV‐2, enabling itself an active target for antiviral development. Herein, we reported the design and synthesis of a new class of peptidomimetics‐constrained α, γ‐AA peptides, based on which a series of aldehyde and ketoamide inhibitors of the M pro of SARS‐CoV‐2 were prepared. The lead compounds showed excellent inhibitory activity in the FRET‐based M pro enzymatic assay not only for the M pro of SARS‐CoV‐2 but also for SARS‐CoV and MERS‐CoV, along with HCoVs like HCoV‐OC43, HCoV‐229E, HCoV‐NL63 and HKU1. The X‐ray crystallographic results demonstrated that our compounds form a covalent bond with the catalytic Cys145. They also demonstrated effective antiviral activity against live SARS‐CoV‐2. Overall, the results suggest that α, γ‐AA peptide could be a promising molecular scaffold in designing novel M pro inhibitors of SARS‐CoV‐2 and other coronaviruses.

Chemistry↗

DOE OSTI2022

(La 0.8 Sr 0.2 ) 0.98 MnO 3-δ -Zr 0.92 Y 0.16 O 2-δ :PrOx for oxygen electrode supported solid oxide cells

(La 0.8 Sr 0.2 ) 0.98 MnO 3-δ (LSM)- Zr 0.92 Y 0.16 O 2-δ (YSZ) has been widely studied as the cathode for solid oxide fuel cells (SOFCs), but its low activity has been a cell performance limiting factor. Herein, LSM-YSZ:PrO x composite is developed as an active electrocatalyst for both oxygen reduction and evolution reactions. A single step PrO x infiltration into LSM-YSZ lowers the polarization resistance (Rp) 10–20 times depending on the test temperature. Distribution of relaxation times (DRT) calculation reveals that adding PrO x affects surface exchange between adsorbed/desorbed oxygen and lattice oxygen, and oxygen dissociative adsorption/desorption. A symmetrical cell with a thin YSZ electrolyte sandwiched between thick LSM-YSZ:PrO x electrode-supports is developed and its oxygen generation performance and stability are evaluated under various current densities and temperatures. Finally, reversible solid oxide cell (ReSOC) performance is also reported for LSM-YSZ:PrO x supported cells with the oxide fuel electrode Sr 0.95 (Ti 0.3 Fe 0.63 Ni 0.07 )O 3-δ (STFN).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Structure-based design of SARS-CoV-2 papain-like protease inhibitors

The COVID-19 pandemic is caused by SARS-CoV-2, an RNA virus with high transmissibility and mutation rate. Given the paucity of orally bioavailable antiviral drugs to combat SARS-CoV-2 infection, there is a critical need for additional antivirals with alternative mechanisms of action. Papain-like protease (PL pro ) is one of the two SARS-CoV-2 encoded viral cysteine proteases essential for viral replication. PL pro cleaves at three sites of the viral polyproteins. In addition, PLpro antagonizes the host immune response upon viral infection by cleaving ISG15 and ubiquitin from host proteins. Therefore, PL pro is a validated antiviral drug target. In this study, we report the X-ray crystal structures of papain-like protease (PL pro ) with two potent inhibitors, Jun9722 and Jun9843 . Subsequently, we designed and synthesized several series of analogs to explore the structure-activity relationship, which led to the discovery of PL pro inhibitors with potent enzymatic inhibitory activity and antiviral activity against SARS-CoV-2. Together, the lead compounds are promising drug candidates for further development.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Nicotine-Inspired, De Novo-Designed SARS-CoV-2 Main Protease Inhibitors Reveal Unique Chemistry for Covalently Conjugating Both Cysteine and Histidine Residues in the Catalytic Dyad

Anecdotal reports about smokers with low SARS-CoV-2 infection rates prompted a search for nicotine and its pyrolysis products as SARS-CoV-2 main protease (M Pro ) inhibitors. From this search, 3-vinylpyridine was discovered as a weak binder for the M Pro S1 subsite and was used subsequently as a de novo starting point for covalent inhibitor design that quickly yielded a highly potent inhibitor, SR-A-174, with an IC 50 value of 60 nM. Representing a novel class of M Pro inhibitors, SR-A-174 features an N,N -diaryl-α,α-dichloroacetamide scaffold that facilitated rapid exploration of alternative covalent warheads and various N-substituents, leading to the identification of multiple inhibitors with potent antiviral activity. Eight such M Pro inhibitor structures were determined, all demonstrating covalent binding to catalytic Cys145 of M Pro . In six determined structures, binding is dominated by the covalent bond plus van der Waals contacts, which contrasts with the extensive hydrogen bond networks formed with peptidomimetic inhibitors such as nirmatrelvir. Strikingly, two N,N -diaryl-α,α-dichloroacetamide inhibitors exhibit an unprecedented dual covalent modification mode of the catalytic dyad, forming bonds to both Cys145 and His41 with a concomitant loss of both chlorides and displacing the inhibitors from the S1 subsite. This dyad-targeting reactivity suggests a novel route for bioconjugation of both cysteine and histidine.

SARS-CoV-2↗

DOE OSTI2021

Michaelis-like complex of SARS-CoV-2 main protease visualized by room-temperature X-ray crystallography

SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (M pro ) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of M pro , a cysteine protease with a catalytic site comprising the noncanonical Cys145–His41 dyad, can help in guiding drug design. Here, a 2.0 Å resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of M pro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH 2 corresponding to the nsp4/nsp5 autocleavage site. The peptide substrate is unambiguously defined in subsites S5 to S3′ by strong electron density. Superposition of the Michaelis-like complex with the neutron structure of substrate-free M pro demonstrates that the catalytic site is inherently pre-organized for catalysis prior to substrate binding. Induced fit to the substrate is driven by P1 Gln binding in the predetermined subsite S1 and rearrangement of subsite S2 to accommodate P2 Leu. The Michaelis-like complex structure is ideal for in silico modeling of the SARS-CoV-2 M pro catalytic mechanism.

3CL protease↗

NASA NTRSDate not supplied

Comparison of Orion Flywheel to Commercially Available Flywheel Device

INTRODUCTION: The chosen exercise device for the Orion Multi-purpose Crew Vehicle (MPCV) for Artemis missions is the Orion Flywheel (OFW), which was selected in 2017 from a pool of exercise devices. The Orion Flywheel is to be installed in the MPCV for its first use during the Artemis II mission and will be utilized for subsequent Artemis missions. The OFW provides the capability to perform both resistive and aerobic exercises while taking up a small volume and not requiring power. Aerobic exercise consists of rowing while resistive exercise includes the deadlift, harness squat, and deadlift high pull among others. The efficacy of the OFW as an exercise countermeasure to spaceflight deconditioning has not yet been fully evaluated. A future HRP-funded study using head-down tilt bed rest is planned to evaluate the efficacy of the OFW to mitigate aerobic and muscular deconditioning. The OFW, made by KBR, is a specialized device that poses high costs for purchase and maintenance. The aim of the study is to determine if a commercially available alternative could be used as a backup for the OFW during the bed rest study or as an alternative in other studies. This study seeks to compare the loading profile and mechanics of a commercial flywheel device (kBox Pro) with the three resistance settings of the OFW using a controlled, instrumented setup to validate its acceptability as a backup. METHODS: An experimental setup was designed to simulate human use of the OFW. Flywheel devices can have varied actuated inertial mass and strap length. The inertial mass refers to the flywheel itself or the object that spins as the result of the movement of the strap. The OFW has three gears actuated with a lever, with the low gear used for aerobic rowing and the medium and high gears used for resistance exercises. These gears correspond to increasing flywheel inertia, which corresponds to a certain number and sizes of inertial plates on a commercial flywheel. The kBox Pro has varied sizes of inertial discs that are installed to the external shaft of the device and can be configured to roughly match the inertia seen in the OFW per gear setting. The strap length can be adjusted to allow for different ranges of motion. The experimental setup allows for the simulation of rowing, harness squats, and deadlift high pulls with corresponding exercise strap lengths. All three OFW gears are to be tested, as well as multiple combinations of kBox discs. The setup was created using a system of pulleys and cables to minimize friction loss. The system is actuated through the dropping of a connected mass which, through the pulley system, pulls the strap of the exercise device upwards as if a human was exercising. A string potentiometer and tensile force transducer are used to measure strap displacement and strap force, respectively. The masses dropped are exercise chains that simulate the decrease in force observed throughout a typical exercise. As the chains are lowered to the ground, they begin to spool and therefore are no longer subjecting the exercise device’s strap to their load. This setup was designed to provide realistic loads and protect the OFW from damage, an important precaution because it’s the only available unit for research and ground operations. Data is to be collected across simulated exercises and with different strap lengths, with the same conditions collected on both the OFW and the kBox Pro. RESULTS: Data collection is ongoing for the kBox and the Orion Flywheel. CONCLUSIONS: Study results will inform if the OFW and a kBox Pro device can be deemed mechanically similar. Depending on the results, additional data collection may be required to assess the user experience between the devices. A key result of this study is a mechanical characterization of the OFW device, demonstrating the load and force profile using a repeatable test method. This data will guide next steps on potential kBox Pro modifications needed to produce a comparable exercise experience to the OFW.

Exercise↗

DOE OSTI2026

Exploration of Nirmatrelvir Derivatives as Optimized SARS‐CoV‐2 Antivirals

Nirmatrelvir (NMV) is a SARS‐CoV‐2 antiviral component of the approved COVID‐19 therapeutic Paxlovid. It is a reversible covalent inhibitor of SARS‐CoV‐2 main protease (M Pro ) that is effluxed from human cells by P‐glycoprotein (P‐gp). To identify NMV analogs with improved potency and reduced P‐gp efflux, a structure–activity relationship campaign was conducted. Warheads alternative to nitrile for engaging the active site cysteine were tested showing aldehyde and dichloroacetamide with better enzyme inhibition potency. Crystal structure of MPI‐136−M Pro shows its aldehyde warhead forming a thiohemiacetal with active Cys145 of M Pro . Several S4 binders were explored revealing that an O‐to‐S shift at the N ‐terminal amide leads to better enzyme inhibition. By exploring different combinations of S2, S3, and S4 binders, two inhibitors with better enzyme inhibition potency than NMV were found. Crystal structure of MPI‐148, with ( S )‐2‐azaspiro[4,5]decane‐3‐carboxylate as an alternative S2 binder, shows extensive hydrogen‐bond networks for locking the inhibitor in active site, explaining high affinity of NMV analogs. Further characterization of cellular M Pro engagement and antiviral potency against SARS‐CoV‐2 revealed four inhibitors with greater potency than NMV in P‐gp‐expressing cells. Studies with the P‐gp inhibitor CP‐100356 showed that these compounds were less sensitive to P‐gp inhibition than NMV, consistent with reduced P‐gp‐mediated efflux.

Alugubelli, Yugendar R. [Texas A&M Drug Discovery ↗

DOE OSTI2021

Leptin modulates gene expression in the heart, cardiomyocytes and the adipose tissue thus mitigating LPS-induced damage

Highlights: • LPS enhanced expression of the leptin gene in mouse tissues and cardiomyocytes. • Leptin downregulated pro-inflammatory genes in vivo and in cardiomyocytes after LPS treatment. • Leptin upregulated expression of antioxidant genes in vivo and in cardiomyocytes after LPS treatment. • Leptin reduced ROS levels in cardiomyocytes after LPS treatment. • Leptin acts to counteract LPS-induced damage in the heart and cardiomyocytes by modulating gene expression. • Anti-inflammatory effects of leptin in transgenic aMUPA mice overexpressing leptin surpassed that of wild type mice. Leptin is an adipokine of pleiotropic effects linked to energy metabolism, satiety, the immune response, and cardioprotection. We have recently shown that leptin causally conferred resistance to myocardial infarction-induced damage in transgenic αMUPA mice overexpressing leptin compared to their wild type (WT) ancestral mice FVB/N. Prompted by these findings, we have investigated here if leptin can counteract the inflammatory response triggered after LPS administration in tissues in vivo and in cardiomyocytes in culture. The results have shown that LPS upregulated in vivo and in vitro all genes examined here, both pro-inflammatory and antioxidant, as well as the leptin gene. Pretreating mice with leptin neutralizing antibodies further upregulated the expression of TNFα and IL-1β in the adipose tissue of both mouse types, and in the αMUPA heart. The antibodies also increased the levels of serum markers for cell toxicity in both mouse types. These results indicate that under LPS, leptin actually reduced the levels of these inflammatory-related parameters. In addition, pretreatment with leptin antibodies reduced the levels of HIF-1α and VEGF mRNAs in the heart, indicating that under LPS leptin increased the levels of these mRNAs. In cardiomyocytes, pretreatment with exogenous leptin prior to LPS reduced the expression of both pro-inflammatory genes, enhanced the expression of the antioxidant genes HO-1, SOD2 and HIF-1α, and lowered ROS staining. In addition, results obtained with leptin antibodies and the SMLA leptin antagonist indicated that endogenous and exogenous leptin can inhibit leptin gene expression. Together, these findings have indicated that under LPS, leptin concomitantly downregulated pro-inflammatory genes, upregulated antioxidant genes, and lowered ROS levels. These results suggest that leptin can counteract inflammation in the heart and adipose tissue by modulating gene expression.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Temporal responsiveness of adipose-derived stem/stromal cell immune plasticity

Highlights: • Adipose-derived stem cells modulate immune responses in a plastic manner. • The persistence of pro- and anti-inflammatory phenotypes was explored over time. • IL-6 was present at all time points; IDO1 was induced after cytokine stimulation. • Phenotypes persisted 96–168 h after returning to control conditions. • Macrophages showed reaction to ASC culture but without time effect. We determined the role of time in adipose-derived stem/stromal cell (ASC) response to a model inflammatory environment. ASCs and other mesenchymal stem/stromal cells exhibit immune plasticity. We evaluated the persistence of pro- and anti-inflammatory phenotypes for ASCs exposed to a sustained or pulse inflammatory stimulus. Using qPCR, flow cytometry, and immunocytochemistry, we monitored the temporal expression and up-regulation patterns of a pro-inflammatory gene (caspase 1), a pleiotropic gene/protein (interleukin 6, IL-6), and an anti-inflammatory gene/protein (indoleamine 2, 3-dioxygenase, IDO1) after exposing ASCs to the cytokines tumor necrosis factor-α and interferon-γ. In response to sustained cytokine stimulation, we discovered that time played a role in the balance of pro- and anti-inflammatory ASC phenotypes. IL-6 was present at all time points for both cytokine-stimulated and non-stimulated conditions, whereas IDO1 was heterogeneously up-regulated in stimulated conditions at later time points. After a pulse stimulus, ASC immunoresponse remained consistent for 96–168 h. As a final measure of immune plasticity, we cultured cytokine-stimulated ASCs with blood-derived macrophages to observe macrophage polarization. While the presence of ASCs altered macrophage phenotype, there was no dependency on the length of ASC cytokine exposure time.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (M pro also known as 3CL pro ) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the M pro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the M pro as potential COVID-19 therapeutics for further testing and possibly clinical trials.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors

Targeted covalent inhibition represents one possible strategy to block the function of SARS-CoV-2 Main Protease (M PRO ), an enzyme that plays a critical role in the replication of the novel SARS-CoV-2. Toward the design of covalent inhibitors, we built a covalent inhibitor dataset using deep learning models followed by high throughput virtual screening of these candidates against M PRO . Two top-ranking inhibitors were selected for mechanistic investigations—one with an activated ester warhead that has a piperazine core and the other with an acrylamide warhead. Specifically, we performed a detailed analysis of the free energetics of covalent inhibition by hybrid quantum mechanics/molecular mechanics simulations. Cleavage of a fragment of the non-structured protein (NSP) from the SARS-CoV-2 genome was also simulated for reference. Simulations show that both candidates form more stable enzyme-inhibitor (E-I) complexes than the chosen NSP. It was found that both the NSP fragment and the activated ester inhibitor react with CYS145 of M PRO in a concerted manner, whereas the acrylamide inhibitor follows a stepwise mechanism. Most importantly, the reversible reaction and the subsequent hydrolysis reaction from E-I complexes are less probable when compared to the reactions with an NSP fragment, showing promise for these candidates to be the base for efficient M PRO inhibitors.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Collective excitations in the tetravalent lanthanide honeycomb antiferromagnet

Thermomagnetic and inelastic neutron-scattering measurements on Na 2 PrO 3 are reported. This material is an antiferromagnetic honeycomb magnet based on the tetravalent lanthanide Pr 4+ and has been proposed to host dominant antiferromagnetic Kitaev interactions. These measurements reveal magnetic fluctuations in Na 2 PrO 3 below an energy of 2 meV as well as crystal-field excitations around 230 meV. Furthermore, the latter energy is comparable to the scale of the spin-orbit interaction and explains both the very small effective moment of around 1.0μB per Pr 4+ and the difficulty to uncover any static magnetic scattering below the ordering transition at T N = 4.6 K. By comparing the low-energy magnetic excitations in Na 2 PrO 3 to those of the isostructural spin-only compound, Na 2 TbO 3 , a microscopic model of exchange interactions is developed that implicates dominant and surprisingly large Heisenberg exchange interactions J≈1.1(1) meV. Although antiferromagnetic Kitaev interactions with K≤0.2J cannot be excluded, the inelastic neutron-scattering data of Na 2 PrO 3 is best explained with a Δ=1.22 easy-axis XXZ exchange anisotropy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗