Resonance Energy Transfer Assay Research Articles

1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors.

N6-methyladenosine (m6A) is the most frequent of the 160 RNA modifications reported so far. Accumulating evidence suggests that the METTL3/METTL14 protein complex, part of the m6A regulation machinery, is a key player in a variety of diseases including several types of cancer, type 2 diabetes, and viral infections. Here we report on a protein crystallography-based medicinal chemistry optimization of a METTL3 hit compound that has resulted in a 1400-fold potency improvement (IC50 of 5 nM for the lead compound 22 (UZH2) in a time-resolved Förster resonance energy transfer (TR-FRET) assay). The series has favorable ADME properties as physicochemical characteristics were taken into account during hit optimization. UZH2 shows target engagement in cells and is able to reduce the m6A/A level of polyadenylated RNA in MOLM-13 (acute myeloid leukemia) and PC-3 (prostate cancer) cell lines.

Graphdiyne/graphene quantum dots for development of FRET ratiometric fluorescent assay toward sensitive detection of miRNA in human serum and bioimaging of living cancer cells

An effective ratiometric fluorescence resonance energy transfer (FRET) assay developed for the sensitive and specific measurement of microRNAs-21 (miRNA-21) using graphdiyne quantum dots (GDQDs) as the new fluorescent probe. GDQDs with uniform size, narrow defined tunable emission peak and good crystallization synthesized via a classical solvothermal approach. In the sensing strategy, GDQDs modified with DNA probe exhibited strong fluorescence (FL) signal at 405 nm, while in the presence of graphene quantum dots (GQDs) duo to Förster-resonance-energy transfer process between GDQDs and GQDs, the fluorescence of GDQDs was efficiently quenched, meanwhile, a new fluorescence signal at 505 nm for GQDs provided. In the presence of miRNA-21, with the hybridization between miRNA-21 and GDQDs modified with DNA probe, the distance of GDQDs (donor) and GQD (acceptor) is increased, and the intensity fluorescent signal of GDQD recovered, which confirmed by decreasing of the average life times for GDQDs-DNA probe from 1.99 to 0.61ns after addition of GQDs, while the average life time increased again to 1.26 ns in the presence of micRNA-21 target. The ratio of the FL intensity (F405/F505) behaved precise and sensitive analytical efficiency for miRNA-21 detection with a good linear range from 5 pM to 200 nM and a detection limit of 0.5 pM (S/N = 3). More importantly, this RNA sensor was feasible to detect target microRNA-21 in the human serum sample and MCF-7 cell lines with a detection limit of 4 cells/10 μL. Furthermore, due to low cytotoxicity of GDQDs multicolour imaging of MDA-MB231 living cancer cells also utilized.

Plant-Derived Cyclotides Modulate κ-Opioid Receptor Signaling.

Cyclotides are plant-derived disulfide-rich peptides comprising a cyclic cystine knot, which confers remarkable stability against thermal, proteolytic, and chemical degradation. They represent an emerging class of G protein-coupled receptor (GPCR) ligands. In this study, utilizing a screening approach of plant extracts and pharmacological analysis we identified cyclotides from Carapichea ipecacuanha to be ligands of the κ-opioid receptor (KOR), an attractive target for developing analgesics with reduced side effects and therapeutics for multiple sclerosis (MS). This prompted us to verify whether [T20K]kalata B1, a cyclotide in clinical development for the treatment of MS, is able to modulate KOR signaling. T20K bound to and fully activated KOR in the low μM range. We then explored the ability of T20K to allosterically modulate KOR. Co-incubation of T20K with KOR ligands resulted in positive allosteric modulation in functional cAMP assays by altering either the efficacy of dynorphin A1–13 or the potency and efficacy of U50,488 (a selective KOR agonist), respectively. In addition, T20K increased the basal response upon cotreatment with U50,488. In the bioluminescence resonance energy transfer assay T20K negatively modulated the efficacy of U50,488. This study identifies cyclotides capable of modulating KOR and highlights the potential of plant-derived peptides as an opportunity to develop cyclotide-based KOR modulators.

Discovery of the first chemical tools to regulate MKK3-mediated MYC activation in cancer

The transcription master regulator MYC plays an essential role in regulating major cellular programs and is a well-established therapeutic target in cancer. However, MYC targeting for drug discovery is challenging. New therapeutic approaches to control MYC-dependent malignancy are urgently needed. The mitogen-activated protein kinase kinase 3 (MKK3) binds and activates MYC in different cell types, and disruption of MKK3-MYC protein–protein interaction may provide a new strategy to target MYC-driven programs. However, there is no perturbagen available to interrogate and control this signaling arm. In this study, we assessed the drugability of the MKK3-MYC complex and discovered the first chemical tool to regulate MKK3-mediated MYC activation. We have designed a short 44-residue inhibitory peptide and developed a cell lysate-based time-resolved fluorescence resonance energy transfer (TR-FRET) assay to discover the first small molecule MKK3-MYC PPI inhibitor. We have optimized and miniaturized the assay into an ultra-high-throughput screening (uHTS) 1536-well plate format. The pilot screen of ~6,000 compounds of a bioactive chemical library followed by multiple secondary and orthogonal assays revealed a quinoline derivative SGI-1027 as a potent inhibitor of MKK3-MYC PPI. We have shown that SGI-1027 disrupts the MKK3-MYC complex in cells and in vitro and inhibits MYC transcriptional activity in colon and breast cancer cells. In contrast, SGI-1027 does not inhibit MKK3 kinase activity and does not interfere with well-known MKK3-p38 and MYC-MAX complexes. Together, our studies demonstrate the drugability of MKK3-MYC PPI, provide the first chemical tool to interrogate its biological functions, and establish a new uHTS assay to enable future discovery of potent and selective inhibitors to regulate this oncogenic complex.

Potential In Vitro Inhibition of Selected Plant Extracts against SARS-CoV-2 Chymotripsin-Like Protease (3CLPro) Activity.

Antiviral treatments inhibiting Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication may represent a strategy complementary to vaccination to fight the ongoing Coronavirus disease 19 (COVID-19) pandemic. Molecules or extracts inhibiting the SARS-CoV-2 chymotripsin-like protease (3CLPro) could contribute to reducing or suppressing SARS-CoV-2 replication. Using a targeted approach, we identified 17 plant products that are included in current and traditional cuisines as promising inhibitors of SARS-CoV-2 3CLPro activity. Methanolic extracts were evaluated in vitro for inhibition of SARS-CoV-2 3CLPro activity using a quenched fluorescence resonance energy transfer (FRET) assay. Extracts from turmeric (Curcuma longa) rhizomes, mustard (Brassica nigra) seeds, and wall rocket (Diplotaxis erucoides subsp. erucoides) at 500 µg mL−1 displayed significant inhibition of the 3CLPro activity, resulting in residual protease activities of 0.0%, 9.4%, and 14.9%, respectively. Using different extract concentrations, an IC50 value of 15.74 µg mL−1 was calculated for turmeric extract. Commercial curcumin inhibited the 3CLPro activity, but did not fully account for the inhibitory effect of turmeric rhizomes extracts, suggesting that other components of the turmeric extract must also play a main role in inhibiting the 3CLPro activity. Sinigrin, a major glucosinolate present in mustard seeds and wall rocket, did not have relevant 3CLPro inhibitory activity; however, its hydrolysis product allyl isothiocyanate had an IC50 value of 41.43 µg mL−1. The current study identifies plant extracts and molecules that can be of interest in the search for treatments against COVID-19, acting as a basis for future chemical, in vivo, and clinical trials.

Proteasomal conformation controls unfolding ability

The 26S proteasome is the macromolecular machine responsible for the bulk of protein degradation in eukaryotic cells. As it degrades a ubiquitinated protein, the proteasome transitions from a substrate-accepting conformation (s1) to a set of substrate-processing conformations (s3 like), each stabilized by different intramolecular contacts. Tools to study these conformational changes remain limited, and although several interactions have been proposed to be important for stabilizing the proteasome's various conformations, it has been difficult to test these directly under equilibrium conditions. Here, we describe a conformationally sensitive Förster resonance energy transfer assay, in which fluorescent proteins are fused to Sem1 and Rpn6, which are nearer each other in substrate-processing conformations than in the substrate-accepting conformation. Using this assay, we find that two sets of interactions, one involving Rpn5 and another involving Rpn2, are both important for stabilizing substrate-processing conformations. Mutations that disrupt these interactions both destabilize substrate-processing conformations relative to the substrate-accepting conformation and diminish the proteasome's ability to successfully unfold and degrade hard-to-unfold substrates, providing a link between the proteasome's conformational state and its unfolding ability.

Preparation and evaluation of lecithin/zein hybrid nanoparticles for the oral delivery of Panax notoginseng saponins

Panax Notoginseng Saponins (PNS) has been widely used in the prevention and treatment of cardiovascular and cerebrovascular diseases such as myocardial infarction, heart failure and cerebral infarction. However, oral administration of PNS showed low bioavailability because of its instability and poor membrane permeability in the gastrointestinal tract. Here, lipoprotein-inspired hybrid nanoparticles of PNS-Lecithin-Zein (PLZ-NPs) were prepared by using a simple phase separation method, which possessed a core-shell structure, where zein was used as protein part to replace the animal origin protein to increase the resistance to acid and enzymes while lecithin was used as the lipid composition to improve the oral absorption of PNS as well as to increase the drug loading capacity of PNS into the nanocarriers. The results of stability test showed that PLZ-NPs had robust enzymolysis resistance ability for acid and digestive enzymes of gastrointestinal environments. The fluorescent resonance energy transfer (FRET) assay confirmed the ability of LZ-NPs to be intactly absorbed by Caco-2 cell monolayer. Cell transport studies demonstrated that the permeability of PLZ-NPs in Caco-2/HT29-MTX co-culture cell model was 1.5-fold that of PNS. Meanwhile, the single-pass intestinal perfusion assay proved the absorption parameter Peff of PLZ-NPs was 1.75 and 1.80 times higher than that of PNS in the ileum and jejunum, respectively. Finally, the in vivo pharmacokinetic experiment showed that the relative oral bioavailability of PLZ-NPs was 1.71-fold that of free PNS in SD rat. In summary, the employment of the Lecithin/Zein hybrid nanoparticles could be considered as a promising approach for PNS analogues.

Cancer-Cell-Derived Hybrid Vesicles from MCF-7 and HeLa Cells for Dual-Homotypic Targeting of Anticancer Drugs.

Here, as a proof of concept, hybrid vesicles (VEs) are developed from two types of cancer cells, MCF-7 and HeLa, for the dual targeting of the anticancer drug doxorubicin (Dox) to cancer cells via homotypic interactions. Hybrid VEs with a size of 181.8± 28.2nm and surface charge of -27.8± 1.9mV are successfully prepared by the fusion of MCF-7 and HeLa VEs, as demonstrated by the fluorescence resonance energy transfer assay. The hybrid VEs exhibit enhanced intracellular uptake both in MCF-7 and HeLa cells. Dox-encapsulated hybrid VEs (Dox-hybrid VEs) also exhibit promising anticancer and antiproliferative activities against MCF-7/multidrug-resistant cells and HeLa cells. In addition, compared to free Dox, the Dox-hybrid VEs exhibit low intracellular uptake and reduced cytotoxicity for RAW264.7 cells. Thus, hybrid VEs with dual-targeting activity toward two types of cancer cells may be useful for the specific targeting of anticancer drugs for improved anticancer effects with reduced nonspecific toxicity.

Generating An Exosome Packaged p38 Inhibitory Peptide To Block GPCR Induced Vascular Inflammation

A key mediator of angiogenesis and inflammatory response in chronic lung disease is the mitogen-activated protein kinase (MAPK), p38α. The typical activation pathway for p38α uses MAP kinase kinase 3 (MKK3), and MKK6 to phosphorylate and activate p38α. However, an atypical p38α signaling pathway activated by a family of pro-inflammatory G-protein coupled receptors (GPCRs) induces a direct interaction between transforming growth factor β activated kinase 1 binding protein-1 (TAB1) and p38α, bypassing MKK3/6-dependent p38α activation. The binding of TAB1 to p38α induces the autophosphorylation of p38α, triggering proinflammatory signaling in the vasculature. Recent studies have highlighted the use of cell-penetrating inhibitors that specifically block atypical p38α signaling, leaving MKK3/6-dependent signaling intact. Using the Xpack Lentiviral expression system, we have generated a stable cell line that expresses red fluorescent protein (RFP) labeled peptide inhibitors in endothelial cells. The Xpack system contains an exosomal packaging motif enabling RFP-linked inhibitor peptides to be targeted for exosomes. Using filter centrifugation and ultracentrifugation we have isolated RFP peptide loaded exosomes/extracellular vesicles. These inhibitor loaded extracellular vesicles can successfully deliver inhibitors to vascular endothelial cells in vitro. Our current studies focus on assessing whether cellular uptake of peptide loaded exosomes can efficiently attenuate GPCR-induced proinflammatory signaling. To investigate this we are using a combination of immunoblotting and live-cell Forster's Resonance Energy Transfer (FRET) assays. We predict that exosomally delivered peptides will inhibit p38 signaling by GPCR ligands in endothelial cells providing a tool to produce large quantities of bioavailable inhibitors that can be developed into therapeutics. These studies demonstrate the potential for exosomal nanocarriers to deliver peptide inhibitors to block GPCR inflammation.

Effects of Parathyroid Hormone on Osteoporotic Fracture Healing in Mice via Non-Phospholipases C-Dependent Protein Kinase C Signaling Pathway

Objectives: This study was aimed to explore the effects of parathyroid hormone (PTH) on osteoporotic fracture healing in mice and the underlying mechanisms. Methods: Microarray analysis was conducted to analyze the gene expression level in MC3T3-E1 cells. Carboxyfluorescein succinimidyl ester (CFSE) staining and flow cytometry was adopted to analyze the proliferation and apopto-sis of MC3T3-E1 cells. qRT-PCR was used to analyze the mRNA expression level. Fluorescence resonance energy transfer (FRET) assay was conducted to detect PKC activity. The bone mineral density (BMD) and bone volume (BV)/total volume (TV) were determined via enzyme-linked immunosorbent assay (ELISA) and microscopic computed tomography (micro-CT). Results: ERK1/2 was abnormally expressed in MC3T3-E1 cells after GlylArg19hPTH (1-34) + KT5720 treatment. GlylArg19hPTH (1-34)+ KT5720 treatment promoted cell proliferation, inhibited cell apoptosis, and upregulatedthe expression of osteogenesis-related genes (ALP, OPN, Runx2 and OPG) in MC3T3-E1 cells, which were due to the activation of the non-PLC-dependent PKC signaling pathway and can be blocked by PKC inhibitor Go6983 or ERK1/2 inhibitor BVD-523. Moreover, the activity of PKC in MC3T3-E1 cells treated with GlylArg19hPTH (1-34) + KT5720 + Go6983 was alleviated by ERK1/2 inhibitor BVD-523. In vivo, specific activation of the non-PLC-dependent PKC signaling pathway increased the serum levels of APL and OPG in mice with osteoporotic fracture, which were reversed by PKC inhibitor Go6983 and ERK1/2 inhibitor BVD-523. Moreover, PKC inhibitor Go6983 and ERK1/2 inhibitor BVD-523 suppressed the elevation of BV/TV and BMD induced by specific activation of the non-PKC-dependent signaling pathway. Conclusions: Taken together, PTH stimulates osteoporotic fracture healing in mice through the non-PLC-dependent PKC signaling pathway in which ERK1/2 exerts a vital role.

G protein‐coupled receptor kinase 2 can enhance β‐arrestin recruitment to the D 2 dopamine receptor in the absence of receptor phosphorylation

The D2 dopamine (DA) receptor (D2R) signals through two main pathways: activation of G proteins and recruitment of β-arrestin. Upon agonist binding to the receptor, an active signaling state is formed that leads to receptor phosphorylation by one or more members of the G protein-coupled receptor kinase (GRK) family. GRK-mediated receptor phosphorylation enhances β-arrestin interactions with many GPCRs, but this mechanism remains unclear for the D2R. We recently identified a single amino acid (F189 (5.38 using Ballesteros-Weinstein numbering)) within the ligand binding site of the D2R that acts as a micro-switch for regulating D2R interactions with β-arrestin (Sanchez-Soto et al., Sci. Signal. 13(617): eaaw5885, 2020). When F189 is mutated to alanine, the D2R-F1895.38A mutant is capable of activating G proteins, but is unable to recruit β-arrestin, i.e., D2R-F1895.38A is a G protein-biased receptor. To investigate the mechanisms underlying the biased signaling of D2R-F1895.38A, its interactions with GRK2 were explored using a variety of bioluminescence resonance energy transfer (BRET) assays. Importantly, we found that D2R-F1895.38A does not recruit GRK2 upon agonist stimulation. This finding suggests that the absence of D2R-F1895.38A -GRK2 interactions may underlie the receptor's inability to recruit β-arrestin. To test this hypothesis, we examined DA-stimulated β-arrestin and GRK2 recruitment using a phosphorylation-defective D2R mutant (Namkung et. al., JBC 284:34103, 2009), the GRK2/3 inhibitor Compound 101, and cells in which expression of one or more GRK subtypes were eliminated by CRISPR-Cas9 technology. Strikingly, the phosphorylation-defective D2R mutant was not impaired in its ability to recruit either GRK2 or β-arrestin. In addition, treatment with Compound 101 resulted in a decrease, but not elimination of DA-stimulated β-arrestin recruitment to the WT D2R, suggesting that, while GRK2 kinase activity is required for enhancement of β-arrestin recruitment, phosphorylation of the D2R is not involved. We further examined the role of GRK2 by using a GRK2 KO cell line and found that, while β-arrestin recruitment to the D2R and D2R internalization were diminished, they were not eliminated. In addition, cells completely lacking all GRK subtypes (Total GRK KO) showed an even lower β-arrestin recruitment and D2R internalization suggesting that multiple GRK subtypes might facilitate D2R-β-arrestin interactions. Finally, overexpression of GRKs2, 3, 4, 5, or 6 in the Total GRK KO cells increased β-arrestin recruitment to the D2R. Taken together, these data suggest that while GRK2, and potentially other GRK subtypes, play a facilitatory role in regulating β-arrestin recruitment to the D2R, and thus can potentially mediate receptor signaling bias, receptor phosphorylation itself does not appear to be involved.

Selective or Specific M1 Muscarinic Receptor Antagonists Exhibit Biased Agonism at the M1 Receptor via β‐arrestin Signaling

Introduction Selective (pirenzepine; PZ) and specific (muscarinic toxin 7; MT7) antagonists of the muscarinic acetylcholine type 1 receptor (M1R) reverse nerve degeneration in rodent models of peripheral neuropathy. These drugs drive axonal outgrowth of adult sensory neurons and signaling is mediated via extracellular-regulated protein kinase (ERK) and β-arrestin. In order to understand the pharmacological mechanism of action of PZ and MT7, we hypothesized that these drugs exhibited biased agonism at the M1R mediated via b-arrestin signaling. Methods Nano bioluminescence resonance energy transfer (NanoBRET) assay: Human embryonic kidney (HEK293) cells co-expressing human M1R-Nluc and Halo-tagged β-arrestin 2 were treated with different doses of M1R agonists (muscarine or carbachol) or antagonists (PZ and MT7)at different time points. NanoBRET assay was employed to measure ligand-induced β-arrestin 2 recruitment to the M1R. Assays were performed in triplicate with 3 independent experiments completed. Data are presented as corrected milli-BRET (mBRET) units. Substrate was added 2 min before BRET detection, and drugs were applied at various time points. Data are reported as the mean ± SD (statistics by 1-way ANOVA with Tukey's post-hoc test). Inositol-phosphate one (IP1) measurement: Intracellular IP1 levels were measured using IP-One assay (Cisbio Bioassays, USA). HEK293 cells co-expressing hM1R-Nluc and Halo-tagged β-arrestin 2 were plated onto 384-well white microplates (20000 cells per well) and were treated with stimulation buffer with or without 1) different doses of M1R agonist (muscarine), 2) M1R antagonists (PZ and MT7) or 3) both M1R antagonist (different doses of PZ) and agonist (muscarine, 1mM) for different time points at 37 °C. Cells were lysed by addition of the supplied buffer containing d2-labeled IP1, followed by addition of terbium cryptate-labeled anti-IP1 antibody, according to the manufacturer's instructions. Plates were incubated for 1 h at room temperature and fluorescence signals were measured at 620 and 665 nm using the Biotek Synergy Neo2 plate reader. HTRF ratio 665 nm/620 nm of each well were extrapolated on the standard curve to obtain IP1 concentrations. Results Both carbachol (Fig. 1A) and muscarine (Fig. 1B) induced Halo-tagged β-arrestin 2 recruitment to hM1R-Nluc in a dose-dependent manner at 5 min of treatment. pirenzepine (Fig. 1C) and MT7 (Fig. 1D) induced Halo-tagged β-arrestin 2 recruitment to hM1R-Nluc in a dose-dependent manner at longer time points (e.g. after 30 min). Interestingly, over short periods, e.g. 2-3 min, PZ and MT7 acted as classical antagonists with blockade of muscarine-induced b-arrestin 2 association with M1R. Unlike MT7 and PZ, muscarine increased IP1 levels in transfected cells (Fig. 2A). Also, PZ dose-dependently inhibited the formation of IP1 following muscarine (1mM) treatment (Fig. 2B). Conclusion Thisstudy for the first time provides molecular evidence to support a role for selective/specific muscarinic receptor antagonists acting as biased agonists at the M1R. This novel signaling pathway may contribute to driving axonal regeneration in adult sensory neurons and could be mobilized for nerve repair in neuropathic disease.

Luminescence lifetime imaging of three-dimensional biological objects.

A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.

Blocking endothelial TRPV4-Nox2 interaction helps reduce ROS production and inflammation, and improves vascular function in obese mice

Obesity induces inflammation and oxidative stress, and ultimately leads to vasodilatory dysfunction in which Transient receptor potential vanilloid type 4 (TRPV4) and Nicotinamide Adenine Dinucleotide Phosphate Oxidase (Nox2) have been reported to be involved. However, little attention has been paid to the role of the TRPV4-Nox2 complex in these problems. The purpose of this study was to figure out the role of the TRPV4-Nox2 complex in obesity-induced inflammation, oxidative stress, and vasodilatory dysfunction. Using fluorescence resonance energy transfer and immunoprecipitation assays, we found enhanced TRPV4 and Nox2 interactions in obese mice. Using q-PCR, fluorescent dye dihydroethidium staining, and myotonic techniques, we found that obesity caused inflammation, oxidative stress, and vasodilatory dysfunction. Using adeno-associated viruses, we found that enhancement or attenuation of TRPV4-Nox2 interaction altered the vaso-function. Based on these findings, we found a small-molecule drug, M12, that interrupted the TRPV4-Nox2 interaction, thereby reducing inflammatory factors and reactive oxygen species production and helping to restore the vasodilatory function. In summary, our results revealed a new mechanism by which obesity-induced inflammation, oxidative stress, and vasodilatory dysfunction is caused by enhanced TRPV4-Nox2 interactions. Using M12 to interrupt the TRPV4-Nox2 interaction may have anti-inflammatory and anti-oxidative stress effects and help restore vasodilatory function and thus provide a new therapeutic approach to obesity.

Live-Cell Analysis of Human Cytomegalovirus DNA Polymerase Holoenzyme Assembly by Resonance Energy Transfer Methods.

Human cytomegalovirus (HCMV) genome replication is a complex and still not completely understood process mediated by the highly coordinated interaction of host and viral products. Among the latter, six different proteins form the viral replication complex: a single-stranded DNA binding protein, a trimeric primase/helicase complex and a two subunit DNA polymerase holoenzyme, which in turn contains a catalytic subunit, pUL54, and a dimeric processivity factor ppUL44. Being absolutely required for viral replication and representing potential therapeutic targets, both the ppUL44–pUL54 interaction and ppUL44 homodimerization have been largely characterized from structural, functional and biochemical points of view. We applied fluorescence and bioluminescence resonance energy transfer (FRET and BRET) assays to investigate such processes in living cells. Both interactions occur with similar affinities and can take place both in the nucleus and in the cytoplasm. Importantly, single amino acid substitutions in different ppUL44 domains selectively affect its dimerization or ability to interact with pUL54. Intriguingly, substitutions preventing DNA binding of ppUL44 influence the BRETmax of protein–protein interactions, implying that binding to dsDNA induces conformational changes both in the ppUL44 homodimer and in the DNA polymerase holoenzyme. We also compared transiently and stably ppUL44-expressing cells in BRET inhibition assays. Transient expression of the BRET donor allowed inhibition of both ppUL44 dimerization and formation of the DNA polymerase holoenzyme, upon overexpression of FLAG-tagged ppUL44 as a competitor. Our approach could be useful both to monitor the dynamics of assembly of the HCMV DNA polymerase holoenzyme and for antiviral drug discovery.

Optimization of expression conditions and determination the proteolytic activity of codon-optimized SARS-CoV-2 main protease in Escherichia coli

The main protease (Mpro) of SARS-CoV-2 is a highly conserved and mutation-resistant coronaviral enzyme, which plays a pivotal role in viral replication, making it an ideal target for the development of novel broad-spectrum anti-coronaviral drugs. In this study, a codon-optimized Mpro gene was cloned into pET-21a and pET-28a expression vectors. The recombinant plasmids were transformed into E. coli Rosetta(DE3) competent cells and the expression conditions were optimized. The highly expressed recombinant proteins, Mpro and Mpro-28, were purified by HisTrapTM chelating column and its proteolytic activity was determined by a fluorescence resonance energy transfer (FRET) assay. The FRET assay showed that Mpro exhibits a desirable proteolytic activity (25 000 U/mg), with Km and kcat values of 11.68 μmol/L and 0.037/s, respectively. The specific activity of Mpro is 25 times that of Mpro-28, a fusion protein carrying a polyhistidine tag at the N and C termini, indicating additional residues at the N terminus of Mpro, but not at the C terminus, are detrimental to its proteolytic activity. The preparation of active SARS-CoV-2 Mpro through codon-optimization strategy might facilitate the development of the rapid screening assays for the discovery of broad-spectrum anti-coronaviral drugs targeting Mpro.

The PRKAR1B p.R115K Variant is Associated with Lipoprotein Profile in African American Youth with Metabolic Challenges.

High childhood obesity rates coincide with increased incidence of nonalcoholic fatty liver disease (NAFLD) and other comorbidities. Understanding the genetics of susceptibility to obesity and its comorbidities could guide intervention. The cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) signaling pathway regulates energy balance, glucose homeostasis, and lipid metabolism. We hypothesized that PKA-related gene variants may be associated with obesity or associated metabolic conditions. We included 457 youths from the Yale Obesity Clinic into the Pathogenesis of Youth-Onset Diabetes cohort (NCT01967849); a variety of clinical tests were performed to characterize NAFLD. Exon sequencing of 54 PKA pathway genes was performed. Variants were confirmed by Sanger sequencing. Clinical data were analyzed, correcting for NAFLD status and body mass index z-score with adjustments for multiple comparisons. Fluorescence resonance energy transfer (FRET) and PKA enzymatic assays were performed in HEK293 cells transfected with the PRKAR1B p.R115K construct. In silico structural analysis for this variant was done. We identified the variant PRKAR1B p.R115K in 4 unrelated, African American patients. Analyses compared this variant group to other African American patients in the cohort. PRKAR1B p.R115K was associated with favorable circulating lipoprotein levels. Analysis of FRET and PKA enzymatic assay showed stronger interaction between the R1β mutant and PKA catalytic subunit Cα and decreased basal PKA activity compared with the wildtype (P < .0001). Structural analysis revealed that p.R115K may hinder conformational changes resulting from cAMP binding at cAMP binding domain A. Data suggest PRKAR1B p.R115K affects cAMP signaling and may favorably modulate lipoprotein profile in African American youth, protecting them from some adverse metabolic outcomes.

Fabrication and bioactivity evaluation of curcumin and paclitaxel loaded lipid nanoparticles of pH-sensitive histidinylated cationic amphiphile

Drug resistance, inefficient cellular uptake and the subservient drug release to increase the intracellular drug concentration inside the tumor cells are the key reasons for low therapeutic efficacy of drug-loaded lipid nanoparticles in cancer therapy. Herein, we report on the design, synthesis and bioactivity evaluation of Curcumin &amp; Paclitaxel (PTX) encapsulated endosomal pH-Sensitive lipid nanoparticles of histidinylated cationic amphiphile (16-GH; 2 in 1 system) to overcome these challenges. Findings in fluorescence resonance energy transfer (FRET) assay and in vitro drug release studies showed a controlled pH dependent fusogenic and drug release properties of the lipid nanoparticles of cationic amphiphile 16-GH respectively. Further in vitro studies revealed that Curcumin &amp; PTX encapsulated nanoparticles of lipid 16-GH significantly inhibited proliferation of tumor cells than healthy cells. These lipid nanoparticles were further analyzed for their effect on 5-bromo-2'-deoxyuridine (BrdU) incorporation, Annexin V-FITC and cell cycle arrest (Sub-G1 phase). Further studies also confirmed that nanoparticles of lipid 16-GH containing Curcumin &amp; PTX displayed significantly enhanced the caspase3/9 activity. Remarkably, nanoparticles of lipid 16-GH containing Curcumin &amp; PTX are efficient in inducing apoptosis. The results in our initial mechanistic studies support the notion that the tumor cell selective cytotoxic capability of the lipid nanoparticles of the presently described endosomal pH-sensitive lipid probably instigates from depolarization of mitochondrial membrane potential and subsequent activation of caspases 3 and 9. The distinguishing feature of the currently described endosomal pH-sensitive system is that it not only efficiently delivers highly potent anti-cancer agents (Curcumin &amp; PTX) to tumor cells, but the lipid nanoparticle drug carrier itself also contributes to inhibiting tumor cell growth. In summary, the presently described lipid nanoparticles are expected to simultaneously delivering combination of drugs to various types of tumor models.

Acetylated Ubiquitin Modulates the Catalytic Activity of the E1 Enzyme Uba1.

Ubiquitin (Ub) signaling requires the covalent passage of Ub among E1, E2, and E3 enzymes. The choice of E2 and E3 enzymes combined with multiple rounds of the cascade leads to the formation of polyubiquitin chains linked through any one of the seven lysines on Ub. The linkage type and length act as a signal to trigger important cellular processes such as protein degradation or the DNA damage response. Recently, proteomics studies have identified that Ub can be acetylated at six of its seven lysine residues under various cell stress conditions. To understand the potential differences in Ub signaling caused by acetylation, we synthesized all possible acetylated ubiquitin (acUb) variants and examined the E1-mediated formation of the corresponding E2∼acUb conjugates in vitro using kinetic methods. A Förster resonance energy transfer assay was optimized in which the Ub constructs were labeled with a CyPet fluorophore and the E2 UBE2D1 was labeled with a YPet fluorophore to monitor the formation of E2∼Ub conjugates. Our methods enable the detection of small differences that may otherwise be concealed in steady-state ubiquitination experiments. We determined that Ub, acetylated at K11, K27, K33, K48, or K63, has altered turnover numbers for E2∼Ub conjugate formation by the E1 enzyme Uba1. This work provides evidence that acetylation of Ub can alter the catalysis of ubiquitination early on in the pathway.

Identification of novel inhibitors of Keap1/Nrf2 by a promising method combining protein\u2013protein interaction-oriented library and machine learning

Protein–protein interactions (PPIs) are prospective but challenging targets for drug discovery, because screening using traditional small-molecule libraries often fails to identify hits. Recently, we developed a PPI-oriented library comprising 12,593 small-to-medium-sized newly synthesized molecules. This study validates a promising combined method using PPI-oriented library and ligand-based virtual screening (LBVS) to discover novel PPI inhibitory compounds for Kelch-like ECH-associated protein 1 (Keap1) and nuclear factor erythroid 2-related factor 2 (Nrf2). We performed LBVS with two random forest models against our PPI library and the following time-resolved fluorescence resonance energy transfer (TR-FRET) assays of 620 compounds identified 15 specific hit compounds. The high hit rates for the entire PPI library (estimated 0.56–1.3%) and the LBVS (maximum 5.4%) compared to a conventional screening library showed the utility of the library and the efficiency of LBVS. All the hit compounds possessed novel structures with Tanimoto similarity ≤ 0.26 to known Keap1/Nrf2 inhibitors and aqueous solubility (AlogP < 5). Reasonable binding modes were predicted using 3D alignment of five hit compounds and a Keap1/Nrf2 peptide crystal structure. Our results represent a new, efficient method combining the PPI library and LBVS to identify novel PPI inhibitory ligands with expanded chemical space.