Novel HIV PR inhibitors with C4-substituted bis-THF and bis-fluoro-benzyl target the two active site
Explore the source record for details and available documents.
Agniswamy, Johnson↗
SEARCH · Engineering Papers
Results for “Active target”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Improved production and purification of 240Am by deuteron-induced activation of 240Pu target
An optimized method for production of 240Am via the 240Pu(d,2n)240Am reaction is reported. The optimized method produced 7.94 × 108 ± 7% atoms 240Am/mg 240Pu/µA-h. The yield and purity of the products from the optimized method are evaluated in context of the intended application to produce material to measure the cross-section for the 240Am(n,f) reaction. The presented method is also compared with other production methods available in the literature. Keywords—240Am production, deuteron-induced reactions, cross-section, target preparation, post-irradiation purification Abbreviations GEA—Gamma Energy Analysis
Morrison, Erin C.↗
Computational design of potent and selective binders of BAK and BAX
Potent and selective binders of the key proapoptotic proteins BAK and BAX have not been described. We use computational protein design to generate high affinity binders of BAK and BAX with greater than 100-fold specificity for their target. Both binders activate their targets when at low concentration, driving pore formation, but inhibit membrane permeabilization when in excess. Crystallography shows that the BAK binder induces BAK unfolding, exposing the α6 helix and BH3 domain. Together, these data suggest that upon binding, BAK or BAX unfold; at high binder concentrations, self-association of the partially folded BAK or BAX proteins is blocked and the membrane remains intact, whereas at low concentrations, dimers form, and the membrane ruptures. Our designed binders modulate apoptosis via direct, specific interactions with BAK and BAX and reveal that for therapeutic strategies targeting BAK and BAX, inhibition requires saturating binder concentrations at the site of action.
Berger, Stephanie↗
Custom scripts used in "Distribution and activity patterns of targeted hypermutation in the global microbiome" (Scripts_DGR) v1
Set of scripts used to identify and analyze DGR loci in metagenomes.
Roux, Simon↗
Ancient origins of allosteric activation in a Ser-Thr kinase
A myriad of cellular events are regulated by allostery; therefore, evolution of this process is of fundamental interest. Here, we use ancestral sequence reconstruction to resurrect ancestors of two colocalizing proteins, Aurora A kinase and its allosteric activator TPX2 (targeting protein for Xklp2), to experimentally characterize the evolutionary path of allosteric activation. Autophosphorylation of the activation loop is the most ancient activation mechanism; it is fully developed in the oldest kinase ancestor and has remained stable over 1 billion years of evolution. As the microtubule-associated protein TPX2 appeared, efficient kinase binding to TPX2 evolved, likely owing to increased fitness by virtue of colocalization. Subsequently, TPX2-mediated allosteric kinase regulation gradually evolved. Surprisingly, evolution of this regulation is encoded in the kinase and did not arise by a dominating mechanism of coevolution.
Science & Technology - Other Topics↗
EpiPro, a Novel, Synthetic, Activity-Regulated Promoter That Targets Hyperactive Neurons in Epilepsy for Gene Therapy Applications
Epileptogenesis is characterized by intrinsic changes in neuronal firing, resulting in hyperactive neurons and the subsequent generation of seizure activity. These alterations are accompanied by changes in gene transcription networks, first with the activation of early-immediate genes and later with the long-term activation of genes involved in memory. Our objective was to engineer a promoter containing binding sites for activity-dependent transcription factors upregulated in chronic epilepsy (EpiPro) and validate it in multiple rodent models of epilepsy. First, we assessed the activity dependence of EpiPro: initial electrophysiology studies found that EpiPro-driven GFP expression was associated with increased firing rates when compared with unlabeled neurons, and the assessment of EpiPro-driven GFP expression revealed that GFP expression was increased ~150× after status epilepticus. Following this, we compared EpiPro-driven GFP expression in two rodent models of epilepsy, rat lithium/pilocarpine and mouse electrical kindling. In rodents with chronic epilepsy, GFP expression was increased in most neurons, but particularly in dentate granule cells, providing in vivo evidence to support the “breakdown of the dentate gate” hypothesis of limbic epileptogenesis. Finally, we assessed the time course of EpiPro activation and found that it was rapidly induced after seizures, with inactivation following over weeks, confirming EpiPro’s potential utility as a gene therapy driver for epilepsy.
60 APPLIED LIFE SCIENCES↗
Active Learning for Rapid Targeted Synthesis of Compositionally Complex Alloys
The next generation of advanced materials is tending toward increasingly complex compositions. Synthesizing precise composition is time-consuming and becomes exponentially demanding with increasing compositional complexity. An experienced human operator does significantly better than a novice but still struggles to consistently achieve precision when synthesis parameters are coupled. The time to optimize synthesis becomes a barrier to exploring scientifically and technologically exciting compositionally complex materials. This investigation demonstrates an active learning (AL) approach for optimizing physical vapor deposition synthesis of thin-film alloys with up to five principal elements. We compared AL-based on Gaussian process (GP) and random forest (RF) models. The best performing models were able to discover synthesis parameters for a target quinary alloy in 14 iterations. We also demonstrate the capability of these models to be used in transfer learning tasks. RF and GP models trained on lower dimensional systems (i.e., ternary, quarternary) show an immediate improvement in prediction accuracy compared to models trained only on quinary samples. Furthermore, samples that only share a few elements in common with the target composition can be used for model pre-training. We believe that such AL approaches can be widely adapted to significantly accelerate the exploration of compositionally complex materials.
Chemistry↗
The PqsE Active Site as a Target for Small Molecule Antimicrobial Agents against Pseudomonas aeruginosa
Not provided.
Biochemistry & Molecular Biology↗
PhenoSelection Manuscript 16S amplicons
Multi-omic analyses can provide a great deal of information on the potential for activity within a microbial community but often lack specificity to link functions to cell and primarily offer potential for function, not true expression of function. Functional assays are necessary for understanding in situ microbial activity to better describe and improve microbiome biology. Targeting enzyme activity through activity-based protein profiling enhances the accuracy of functional studies. Here, we introduce PhenoSelection, a pipeline of coupling activity-based probing with fluorescence-activated cell sorting and downstream activity assays to isolate and examine viable populations of cells expressing a function of interest. We applied PhenoSelection to a soil microbiome to enrich for communities with elevated activity for lignocellulose-degradation phenotypes. PhenoSelection was able to separate and identify taxonomic members with activity for glycosyl hydrolases, and expanding to various probes for other function, this process can be applied to unique phenotypes of interest.
59 BASIC BIOLOGICAL SCIENCES↗
Probing the SARS-CoV-2 main protease active site as a target to inhibit viral replication
SARS-CoV-2 replication involves the synthesis of two large proteins, which are inactive and harmless until the viral main protease enzyme (3CL M pro ) uses them as substrates, cleaving them into many smaller, functional products. Dr Andrey Kovalevsky and his team from Oak Ridge National Laboratory propose a design of novel inhibitors and the repurposing of clinical drugs developed to treat other diseases for the treatment of COVID-19. Finally, the team uses room temperature crystallography with X-rays and neutrons to guide structure-based and computer-assisted drug design and to assess the ability of drugs to inhibit the SARS-CoV-2 main protease, causing virus replication to stop.
Kneller, Daniel↗
FAK-targeting PROTAC demonstrates enhanced antitumor activity against KRAS mutant non-small cell lung cancer
Focal adhesion kinase (FAK) has been established as a promising therapeutic target for KRAS mutant non-small cell lung cancer (NSCLC). However, phase II clinical trials of a FAK inhibitor (Defactinib) have only shown modest antitumor activity. To address this challenge, here we report the use of a FAK-targeting proteolysis targeting chimera (D-PROTAC) to treat KRAS mutant NSCLC. We validated that D-PROTAC could efficiently eliminate FAK protein via the ubiquitin-proteasome pathway in KRAS mutant NSCLC A427 cells, causing over 90% degradation at 800 nM. After comparing both in vitro and in vivo therapeutic efficacies, we demonstrated that D-PRTOAC outperformed Defactinib in inhibiting tumor growth. Specifically, D-PROTAC at 800 nM reduced cell viability, migration, and invasion by ∼80%. Furthermore, a ∼85% suppression of tumor growth was elicited by D-PROTAC when intratumorally administrated at 10 mg/kg in subcutaneous A427-bearing mice. These results thus demonstrate for the first time that PROTACs may serve as promising therapeutic agents for the intractable NSCLC harboring KRAS mutations.
60 APPLIED LIFE SCIENCES↗
The GRAS protein RAM1 interacts with WRI transcription factors to regulate plant genes required for arbuscule development and function
During arbuscular mycorrhiza (AM) symbiosis AM fungi form tree-shaped structures called arbuscules in root cortex cells of host plants. Arbuscules and their host cells are central for reciprocal nutrient exchange between the symbionts.REQUIRED FOR ARBUSCULAR MYCORRHIZATION1(RAM1) encodes a GRAS protein crucial for transcriptionally regulating plant genes needed for arbuscule development and nutrient exchange. Similar to other GRAS proteins, RAM1 likely does not bind to DNA and how RAM1 activates its target promoters remained elusive. Here, we demonstrate that RAM1 interacts with five AM-induced APETALA 2 (AP2) transcription factors of the WRINKLED1-like family called CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), WRI3, WRI5a, WRI5b, and WRI5c via a C-terminal domain containing the M2/M2a motif. This motif is conserved and enriched in WRI proteins encoded by genomes of AM-competent plants. RAM1 together with any of these WRI proteins activates the promoters of genes required for symbiotic nutrient exchange, namelyRAM2,STUNTED ARBUSCULES (STR),andPHOSPHATE TRANSPORTER 4 (PT4), inNicotiana benthamianaleaves. This activation as well as target promoter induction inLotus japonicushairy roots depends onMYCS(MYCORRHIZA SEQUENCE)-elements andAW-boxes, previously identified as WRI-binding sites. TheWRIgenes are activated in two waves: Transcription ofRAM1,CBX1,andWRI3is coregulated by calcium- and calmodulin-dependent protein kinase-activated CYCLOPS, through theAMCYC-REin their promoter, and DELLA, whileWRI5a,b,andcpromoters containMYCS-elements andAW-boxes and can be activated by RAM1 heterocomplexes with CBX1 or WRI3. We propose that RAM1 provides an activation domain to DNA-binding WRI proteins to activate genes with central roles in AM development and function.
Science & Technology - Other Topics↗
Csx3 is a cyclic oligonucleotide phosphodiesterase associated with type III CRISPR–Cas that degrades the second messenger cA 4
Cas10 is the signature gene for type III CRISPR–Cas surveillance complexes. Unlike type I and type II systems, type III systems do not require a protospacer adjacent motif and target nascent RNA associated with transcriptionally active DNA. Further, target RNA recognition activates the cyclase domain of Cas10, resulting in the synthesis of cyclic oligoadenylate second messengers. These second messengers are recognized by ancillary Cas proteins harboring CRISPR-associated Rossmann fold (CARF) domains and regulate the activities of these proteins in response to invading nucleic acid. Csx3 is a distant member of the CARF domain superfamily previously characterized as a Mn 2+ -dependent deadenylation exoribonuclease. However, its specific role in CRISPR–Cas defense remains to be determined. Here we show that Csx3 is strongly associated with type III systems and that Csx3 binds cyclic tetra-adenylate (cA 4 ) second messenger with high affinity. Further, Csx3 harbors cyclic oligonucleotide phosphodiesterase activity that quickly degrades this cA 4 signal. In addition, structural analysis identifies core elements that define the CARF domain fold, and the mechanistic basis for ring nuclease activity is discussed. Overall, the work suggests that Csx3 functions within CRISPR–Cas as a counterbalance to Cas10 to regulate the duration and amplitude of the cA 4 signal, providing an off ramp from the programmed cell death pathway in cells that successfully cure viral infection.
36 MATERIALS SCIENCE↗
Transcriptional Regulatory Networks Involved in C3–C4 Alcohol Stress Response and Tolerance in Yeast
Alcohol toxicity significantly impacts the titer and productivity of industrially produced biofuels. To overcome this limitation, we must find and use strategies to improve stress tolerance in production strains. Previously, we developed a multiplex navigation of a global regulatory network (MINR) library that targeted 25 regulatory genes that are predicted to modify global regulation in yeast under different stress conditions. Herein, we expanded this concept to target the active sites of 47 transcriptional regulators using a saturation mutagenesis library. The 47 targeted regulators interact with more than half of all yeast genes. We then screened and selected for C3–C4 alcohol tolerance. We identified specific mutants that have resistance to isopropanol and isobutanol. Notably, the WAR1_K110N variant improved tolerance to both isopropanol and isobutanol. In addition, we investigated the mechanisms for improvement of isopropanol and isobutanol stress tolerance and found that genes related to glycolysis play a role in tolerance to isobutanol, while changes in ATP synthesis and mitochondrial respiration play a role in tolerance to both isobutanol and isopropanol. Overall, this work sheds light on basic mechanisms for isopropanol and isobutanol toxicity and demonstrates a promising strategy to improve tolerance to C3–C4 alcohols by perturbing the transcriptional regulatory network.
09 BIOMASS FUELS↗
Guidance for Integrating Energy Justice and Equity in Building Technology Deployment Programs: Tracking, Reporting, and Maximizing the Flow of Benefits from Building System Technology Deployment Activities to Disadvantaged Communities and Target Sectors
The Federal Justice40 Initiative directs at least 40% of the overall benefits of certain clean energy investments to flow to disadvantaged communities and requires that all federal programs covered by Justice40 consult stakeholders to determine the program benefits, and that the flow of benefits to disadvantaged communities is tracked and reported. Unequal distribution of benefits, in terms of access to clean energy research, design, development, and deployment, can disproportionately benefit or burden certain communities. This can result in higher rates of pollution, negative health effects, and increased energy burdens and insecurities in disadvantaged communities. Programs focused on decarbonizing the built environment can enhance health, quality of life, and economic opportunities for impacted communities. This guidance document, developed by Pacific Northwest National Laboratory and funded by the U.S. Department of Energy’s Building Technologies Office, provides best practices and approaches for incorporating energy justice and equity principles into building technology deployment activities. It provides best practices and recommendations for communicating with and involving disadvantaged communities and target building sectors in program activities, along with methods to monitor and report the distribution of benefits to these sectors. This document lays out a set of strategies, metrics, and best practices that can be implemented over time to apply energy justice and equity approaches, whether the program is just starting out or ongoing. Although this guidance was designed for Building Technologies Office technology deployment programs, the best practices, recommendations, and methods can be valuable to any program concerned with the equitable deployment of clean energy technologies. The goal of this project is to enable the equitable development, deployment, and adoption of clean energy technologies and practices.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
SpinQuest Polarized Target System
The SpinQuest experiment at Fermilab uses a solid-state polarized ammonia target held at a magnetic field of 5 T, immersed in liquid helium-4, which is held at approximately 1K by the evaporation refrigerator. The refrigerator provides the required cooling power during the dynamic nuclear polarization (DNP) process and the high intensity interaction with the 120 GeV proton beam from the Fermilab main injector. The refrigerator was designed in compliance with the American Society of Mechanical Engineers (ASME) to operate safely at Fermilab. The high pumping capacity ($17,000 \:m^3/h$) roots stack provides the required pumping speed during DNP production data taking and a custom-made radiation hard flow control valve regulates the refrigerator temperature during the thermal equilibrium calibration measurements. The frequency of the microwave generator, an Extended Interaction Oscillator (EIO), is automated to keep the maximum polarization while the (Nuclear Magnetic Resonance) NMR system continuously measures the polarization of the target material. In this talk, an overview of the SpinQuest polarized target system will be presented as well as a brief report of recent commissioning activities and target performance during the early production runs in 2024.
Bandara, Vibodha [Colombo U.]↗
Targeted inhibition of MASTL kinase activity induces apoptosis in breast cancer
Microtubule-associated serine/threonine kinase-like (MASTL) (or Greatwall kinase (GWL)) is an important cell cycle regulating kinase that regulates the G2-M transition. Uncontrolled MASTL activity is implicated in breast cancer progression. To date, very few inhibitors have been reported against this protein. Here, structure-based computational modeling indicates that the natural product flavopiridol (FLV) binds strongly to MASTL and these results are validated using molecular dynamics simulation studies. Further, an in vitro kinase assay reveals an EC 50 (effective concentration) value of FLV to be 82.1 nM and a better IC 50 compared to the positive reference compound, staurosporine. FLV is found to inhibit MASTL kinase activity, arresting the cell growth in the G1 phase and inducing apoptosis in breast cancer cells. Consistent with these results differential gene expression obtained using RNA sequencing studies, and validated by RT PCR and immunoblot analysis, indicate that MASTL inhibition induces cell cycle arrest and apoptotic-related genes. Furthermore, metastasis- and inflammation- related genes are downregulated. Thus, the deregulation of MASTL signaling pathways on targeted inhibition of its kinase activity is revealed. This study lays a strong foundation for investigating FLV as a lead compound in breast cancer therapeutics.
60 APPLIED LIFE SCIENCES↗
Massively parallel, computationally guided design of a proenzyme
Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner. Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.
59 BASIC BIOLOGICAL SCIENCES↗