N-tert-Butoxycarbonyl-N-(2-(tritylthio)ethoxy)glycine as a Building Block for Peptide Ubiquitination.

N-Boc-N-(2-(tritylthio)ethoxy)glycine has been developed as a building block for peptide ubiquitination, which is fully compatible with solid-phase Fmoc chemistry and common peptide modifications including phosphorylation, methylation, acetylation, biotinylation, and fluorescence labeling. The optimal conditions for peptide cleavage and auxiliary removal were obtained. The utility of this building block in peptide ubiquitination was demonstrated by the synthesis of seven ubiquitinated histone and Tau peptides bearing various modifications. Cys residues were well tolerated and did not require orthogonal protection. The structural integrity and folding of the synthesized ubiquitinated peptides were confirmed by enzymatic deubiquitination of a fluorescently labeled ubiquitin conjugate. The synthetic strategy using this building block provides a practical approach for the preparation of ubiquitinated peptides with diverse modifications.

Effects of Benzo[a]pyrene on Food Metabolism and Reproductive Endocrine and Ovarian Development in Female Scallop Chlamys farreri at Different Reproductive Stages.

Benzo[a]pyrene (B[a]P), a polycyclic aromatic hydrocarbon (PAH) with the most carcinogenic effects of all the PAHs, has multiple toxic effects on marine bivalves. We investigated the interference mechanism of B[a]P on food metabolism (sugars, proteins, and sugars), and on reproductive endocrine and ovarian development in female scallops (Chlamys farreri). Scallops were exposed to different concentrations of B[a]P concentrations of 0, 0.38, 3.8, and 38 µg/L throughout gonadal development. Total cholesterol and triglyceride contents in the digestive glands were increased, and their synthesis genes were upregulated. The plasma glucose contents decreased with the inhibition of glycogen synthesis genes and the induction of glycolysis genes in the digestive gland. The results showed that B[a]P had endocrine-disrupting effects on scallops, that it negatively affected genes related to ovarian cell proliferation, sex differentiation, and egg development, and that it caused damage to ovarian tissue. Our findings supplement the information on B[a]P disruption in gonadal development of marine bivalves. Environ Toxicol Chem 2024;43:748-761. © 2023 SETAC.

Occurrence and carcinogenic potential of airborne PBDD/Fs and PCDD/Fs around a large-scale municipal solid waste incinerator: A long-term passive air sampling study.

Municipal solid waste incinerator (MSWI) not only is deemed one of the uppermost sources of polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs), but also produces substantial amount of polybrominated dibenzo-p-dioxins/furans (PBDD/Fs) owing to the existence of brominated flame retardants (BFRs) in the waste. So far, however, PBDD/Fs in the vicinal environments of MSWI and their associated risks remain rarely studied. Based on a one-year passive air sampling (PAS) scheme, we investigated airborne PBDD/Fs and PCDD/Fs around a large-scale MSWI that has been operated for multi-years. Both the concentrations of PBDD/Fs and PCDD/Fs showed spatially decreasing trends with the distance away from the MSWI, confirming the influence of the MSWI on the dioxin levels in its ambient air. But its influence on PBDD/Fs was less because PBDD/Fs exhibit lower volatility and therefore lower gaseous concentrations than PCDD/Fs. Compared to the existing global data of airborne PCDD/Fs and PBDD/Fs, our data of the MSWI vicinity were at medium levels, despite PAS samples only represent the concentrations of gaseous dioxins in theory. The seasonal data suggest that meteorological conditions exerted apparent influences over the concentrations and sources of airborne dioxins around the MSWI. As for PCDD/Fs, the MSWI was diagnosed as their uppermost source, followed by local traffic and volatilization/deposition. Whereas the top three PBDD/F sources were related to PBDEs, bromophenol/bromobenzene, and traffic vehicles, respectively. The bioassay-derived TEQs based on the aryl hydrocarbon receptor activation of airborne dioxins around the MSWI were one or two orders of magnitudes higher than their concentration-based TEQs, and the corresponding carcinogenic risks at some MSWI-vicinal sites exceeded the acceptable threshold proposed by the U. S. EPA (10-6 âˆ¼ 10-4) and deserve continuous attention.

Liposomal Permeation Assay for Droplet-Scale Pharmacokinetic Screening.

Combinatorial library screening increasingly explores chemical space beyond the Ro5 (bRo5), which is useful for investigating "undruggable" targets but suffers compromised cellular permeability and therefore bioavailability. Moreover, structure-permeation relationships for bRo5 molecules are unclear partially because high-throughput permeation measurement technology for encoded combinatorial libraries is still nascent. Here, we present a permeation assay that is scalable to combinatorial library screening. A liposomal fluorogenic azide probe transduces permeation of alkyne-labeled molecules into small unilamellar vesicles via copper-catalyzed azide-alkyne cycloaddition. Control alkynes (e.g., propargylamine, various alkyne-labeled PEGs) benchmarked the assay. Cell-permeable macrocyclic peptides, exemplary bRo5 molecules, were alkyne labeled and shown to retain permeability. The assay was miniaturized to microfluidic droplets with high assay quality (Z' ≥ 0.5), demonstrating excellent discrimination of photocleaved known membrane-permeable and -impermeable model library beads. Droplet-scale permeation screening will enable pharmacokinetic mapping of bRo5 libraries to build predictive models.

Evaluating Translational Efficiency of Noncanonical Amino Acids to Inform the Design of Druglike Peptide Libraries.

Advances in genetic code reprogramming have allowed the site-specific incorporation of noncanonical functionalities into polypeptides and proteins, providing access to wide swaths of chemical space via in vitro translation techniques like mRNA display. Prior efforts have established that the translation machinery can tolerate amino acids with modifications to both the peptide backbone and side chains, greatly broadening the chemical space that can be interrogated in ligand discovery efforts. However, existing methods for confirming the translation yield of new amino acid building blocks for these technologies necessitate multistep workups and, more importantly, are not relevant for measuring translation within the context of a combinatorial library consisting of multiple noncanonical amino acids. In this study, we developed a luminescence-based assay to rapidly assess the relative translation yield of any noncanonical amino acid in real time. Among the 59 amino acids tested here, we found that many translate with high efficiency, but translational yield is not necessarily correlated to whether the amino acid is proteinogenic or has high tRNA acylation efficiency. Interestingly, we found that single-template translation data can inform the library-scale translation yield and that shorter peptide libraries are more tolerant of lower-efficiency amino acid monomers. Together our data show that the luminescence-based assay described herein is an essential tool in evaluating new building blocks and codon table designs within mRNA display toward the goal of developing druglike peptide-based libraries for drug discovery campaigns.

Polybrominated dibenzo-p-dioxins/furans and their chlorinated analogues in sediments from a historical hotspot for both brominated flame retardants and organochlorine pesticides.

Polybrominated dibenzo-p-dioxin/furans (PBDD/Fs) and polychlorinated dibenzo-p-dioxin/furans (PCDD/Fs) in the environment are closely related to their precursors, brominated flame retardants (BFRs) and organochlorine pesticides (OCPs). However, their change trends following the regulation of BFRs and OCPs remain incompletely characterized. Here, we examined PBDD/Fs and PCDD/Fs in sediments from a historical hotspot for both BFRs and OCPs, namely the Pearl River Delta (PRD), China. PBDD/Fs showed ubiquity in these samples but significantly lower concentrations than PCDD/Fs. Spatially, the occurrence of PBDD/Fs was positively correlated with local development levels and sediments from highly urbanized/industrialized areas showed higher and increasing PBDD/F concentrations. Polybrominated diphenyl ether (PBDE)-related products/industries were the greatest PBDD/F contributors to the PRD, followed by bromo-phenol/benzene-related products/industries. PCDD/Fs in PRD sediments showed significant positive correlations with local grain planting area, yield, and pesticide consumption. The historical use of pentachlorophenol (PCP)/PCP-Na and biomass open-burning were the leading PCDD/F sources of the PRD agricultural/rural areas, where the concentrations and toxic equivalent quantities (TEQs) of PCDD/Fs in sediments changed very little over the past decade. Anthropogenic thermal processes involved in metallurgy, waste incineration, and vehicles were the greatest PCDD/F contributors in the PRD urban/industrial areas, where the PCDD/F concentrations in sediments almost doubled over the last decade. This finding indicates the increasing PCDD/F contributions of industrial and municipal activities in the PRD, despite the implementation of strict emission standards. Over sixty percent of the samples showed TEQs that surpassed the low-risk threshold specified for mammalian life by the U.S. EPA (2.5 pg TEQ g-1) and warrant continuous attention.

Polybrominated dibenzo-p-dioxins/furans (PBDD/Fs) in soil around municipal solid waste incinerator: A comparison with polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs).

Polybrominated dibenzo-p-dioxins/furans (PBDD/Fs) and polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs) share similar toxicities and thermal origins, e.g., municipal solid waste incinerator (MSWI). Recently, PBDD/Fs from MSWI attracted rising concern because their important precursors, i.e., brominated flame retardants (BFRs), were frequently found in various wastes for landfill or MSWI feedstock. So far, however, little is known about PBDD/Fs and their associated risks in the vicinal environments of MSWI. Here we analyzed PBDD/Fs and PCDD/Fs in 29 soil samples collected around a multiyear large-scale MSWI, and compared their spatial distributions, sources and risks. PBDD/Fs demonstrated comparable concentrations and toxic equivalent quantities (TEQs) to PCDD/Fs in these samples. Spatially, both the concentrations of PBDD/Fs and PCDD/Fs decreased outwards from the MSWI, and exhibited significant linear correlations with the distances from the MSWI in the southeast downwind soil, suggesting the influence of the MSWI on its vicinal soil environment. However, the existence of other dioxin sources concealed its influence beyond 6 km. PBDD/Fs in the soils were characterized by highly-brominated PBDFs, especially Octa-BDF, and their sources were diagnosed as the MSWI and diesel exhaust; PCDD/Fs, however, were dominated by highly-chlorinated PCDDs, particularly Octa-CDD, and were contributed individually or jointly by the MSWI, automobile exhaust and pentachlorophenol (PCP)/Na-PCP. The non-carcinogenic risks of dioxins in all the soil samples were acceptable, but their carcinogenic risks in 17% of the samples were unacceptable. These samples were all located close to the MSWI and highways, therefore, the land use of these two high-risk zones should be cautiously planed.

A novel method to produce synthetic murine CXCL10 for efficient screening of functional variants.

Antitumor immune responses depend on the infiltration of solid tumors by effector T cells, a process guided by chemokines. In particular, the chemokine CXCL10 has been shown to play a critical role in mediating recruitment of CXCR3 + cytolytic T and NK cells in tumors, though its use as a therapeutic agent has not been widely explored. One of the limitations is due to the rapid inactivation of CXCL10 by dipeptidyl peptidase 4 (DPP4), a broadly expressed enzyme that is active in plasma and other bodily fluids. In the present study, we describe a novel method to produce synthetic CXCL10 that is resistant to DPP4 N-terminal truncation. Using a Fmoc solid-phase peptide synthesis approach, synthetic murine WT CXCL10 was produced, showing similar biochemical and biological properties to the recombinant protein. This synthesis method supported production of natural (amino acid substitution, insertion or deletion) and non-natural (chemical modifications) variants of CXCL10. In association with a functional screening cascade that assessed DPP4-mediated cleavage, CXCR3 signaling potency and chemotactic activity, we successfully generated 20 murine CXCL10 variants. Among those, two non-natural variants with N-methylated Leu3 (MeLeu3) and a reduced amide bond between Pro2 and Leu3 (rLeu3), respectively, showed resistance to DPP4 truncation but decreased CXCR3 signaling and chemotactic activity. Interestingly, MeLeu3 and rLeu3 CXCL10 behaved as DPP4 inhibitors, preventing the truncation of WT CXCL10. This study highlights the potential of using Fmoc solid-phase chemistry in association with biochemical and biological characterization to rapidly identify CXCL10 variants with desired properties. These novel methods unlock the opportunity to develop DPP4 resistant CXCL10 variants, as well as other chemokine substrates, while maintaining chemotactic properties.

Ribosomal Synthesis of Macrocyclic Peptides with ß2- and ß2,3-Homo-Amino Acids for the Development of Natural Product-Like Combinatorial Libraries.

The development of large, natural-product-like, combinatorial macrocyclic peptide libraries is essential in the quest to develop therapeutics for "undruggable" cellular targets. Herein we report the ribosomal synthesis of macrocyclic peptides containing one or more ß2-homo-amino acids (ß2haa) to enable their incorporation into mRNA display-based selection libraries. We confirmed the compatibility of 14 ß2-homo-amino acids, (S)- and (R)-stereochemistry, for single incorporation into a macrocyclic peptide with low to high translation efficiency. Interestingly, N-methylation of the backbone amide of ß2haa prevented the incorporation of this amino acid subclass by the ribosome. Additionally, we designed and incorporated several α,ß-disubstituted ß2,3-homo-amino acids (ß2,3haa) with different R-groups on the α- and ß-carbons of the same amino acid. Incorporation of these ß2,3haa enables increased diversity in a single position of a macrocyclic peptide without significantly increasing the overall molecular weight, which is an important consideration for passive cell permeability. We also successfully incorporated multiple (S)-ß2hAla into a single macrocycle with other non-proteinogenic amino acids, confirming that this class of ß-amino acid is suitable for development of large scale macrocyclic peptide libraries.

Development of orthogonally protected hypusine for solid-phase peptide synthesis.

An orthogonally protected hypusine reagent was developed for solid-phase synthesis of hypusinated peptides using the Fmoc/t-Bu protection strategy. The reagent was synthesized in an overall yield of 27% after seven steps from Cbz-Lys-OBzl and (R)-3-hydroxypyrrolidin-2-one. The side-chain protecting groups (Boc and t-Bu) are fully compatible with standard Fmoc chemistry and can be readily removed during the peptide cleavage step. The utility of the reagent was demonstrated by solid-phase synthesis of hypusinated peptides.

LAS0811: from combinatorial chemistry to activation of antioxidant response element.

The antioxidant response element (ARE) and its transcription factor, nuclear factor-erythroid 2 p45-related factor 2 (Nrf2), are potential targets for cancer chemoprevention. We sought to screen small molecules synthesized with combinatorial chemistry for activation of ARE. By high-throughput screening of 9400 small molecules from 10 combinatorial chemical libraries using HepG2 cells with an ARE-driven reporter, we have identified a novel small molecule, 1,2-dimethoxy-4,5-dinitrobenzene (LAS0811), as an activator of the ARE. LAS0811 upregulated the activity of NAD(P)H:quinone oxidoreductase 1 (NQO1), a representative antioxidative enzyme regulated by ARE. It enhanced production of an endogenous reducing agent, glutathione (GSH). In addition, LAS0811 induced expression of heme oxygenase 1 (HO1), which is an ARE-regulated enzyme with anti-inflammatory activity. Furthermore, LAS0811 reduced cell death due to the cytotoxic stress of a strong oxidant, t-butyl hydroperoxide (t-BOOH). Mechanistically, LAS0811 upregulated the expression of Nrf2 and promoted its translocation into the nuclei leading to subsequent ARE activation. Taken together, LAS0811 is a novel activator of the ARE and its associated detoxifying genes and, thus, a potential agent for cancer chemoprevention.

Discovery of 5-substituted 2-amino-4-chloro-8-((4-methoxy-3,5-dimethylpyridin-2-yl)methyl)-7,8-dihydropteridin-6(5H)-ones as potent and selective Hsp90 inhibitors.

A new series of compounds, 5-substituted 2-amino-4-chloro-8-((4-methoxy-3,5-dimethylpyridin-2-yl)methyl)-7,8-dihydropteridin-6(5H)-ones, have been designed and identified as potent and selective inhibitors of Hsp90. These compounds demonstrated nanomolar potency toward both Hsp90-regulated Her2 degradation and the growth of a panel of human tumor cell lines in cell-based assays. High selectivity of these compounds toward Hsp90 was evident given that they did not inhibit a panel of 34 kinases at 10microM. The structure-activity relationship (SAR) of this series is reported here.

Evaluation of ketone-oxime method for developing therapeutic on-demand cleavable immunoconjugates.

The use of antibody molecules in immunoassay, molecular targeting, or detection techniques encompasses a broad variety of applications affecting nearly every field of medical science. In cancer therapy, monoclonal antibodies (mAb) have been used as vehicles to deliver radionuclides, toxins, or drugs to the target cancer cells. New conjugation methods are most needed to conjugate a wide variety of targeting small molecules and peptidomimatic compounds. Here, we exploited a keto-oxime method for conjugation of protease susceptible linkers to an antibody. This modified method involves two steps: (i) introduction of methyl ketone linkers (referred to as linker moiety) to the primary amines present in the antibody and (ii) conjugation of ketone linkers to aminoxy functional group present in the conjugated moiety (referred to as functional moiety). We have optimized this conjugation method and shown that approximately 10 functional moieties can be conjugated to antibody. Conjugation was verified by MALDI-TOF MS and Western blot analysis. The acidic pH conditions used in this method did not change the immune reactivity of the Ab. In addition, in vitro protease susceptibility assay was performed to validate this method for prodrug release assay as well as to remove excess radioimmune conjugates from circulation. This orthogonal method is compatible with peptides containing a thiol, amino, or carboxyl groups in the conjugation moiety.

Development of tissue plasminogen activator specific "on demand cleavable" (odc) linkers for radioimmunotherapy by screening one-bead-one-compound combinatorial peptide libraries.

New strategies are needed to protect normal organs from radiation in cancer radioimmunotherapy (RIT). This can be achieved by rapid clearance of radiometal in the circulation after accumulation of radioimmunoconjugates (RIC) in the tumor. Our strategy is to place highly efficient and specific cleavable linkers between radiometal chelates and the tumor targeting agents. Such linkers must be resistant to cleavage by enzymes present in the plasma and the tumor. After radiotargeting agents have accumulated in the tumor, a cleaving agent can be administered "on demand" to cleave a specific linker, resulting in the release of radiometal from the circulating RIC in a form that will have rapid renal clearance. We have selected TNKase, a thrombolytic agent approved for patient use, as our model on-demand cleaving agent. To identify TNKase-specific linkers, we screened fluorescent-quenched random "one-bead-one-compound" (OBOC) combinatorial peptide libraries. d-Amino acid containing peptides that were specific for TNKase but were resistant to cleavage by plasma and tumor-associated proteases were identified. One of these peptide substrates (rqYKYkf) was used to link the DOTA chelate to ChL6, a monoclonal antibody known to target breast cancer. This antibody conjugate was stable in plasma for 7 days while preserving the immunoreactivity to intact tumor cells. The addition of TNKase at clinical achievable plasma level (10 mug/mL) resulted in the release of 28% of the radiometal from the radioimmunoconjugate within 72 h. This lead linker, after further optimization to increase its response to TNKase, may be useful in the development of more effective radioimmunotherapeutic and radioimaging agents.

Synthesis and reactions of 7-fluoro-4-methyl-6-nitro-2-oxo-2H-1-benzopyran-3-carboxylic acid: a novel scaffold for combinatorial synthesis of coumarins.

7-Fluoro-4-methyl-6-nitro-2-oxo-2H-1-benzopyran-3-carboxylic acid has been prepared as a novel scaffold for combinatorial synthesis of coumarins. The scaffold has three points of diversity. The optimal conditions for its reactions with different nucleophiles in solid phase were obtained. Sixteen coumarin derivatives with different structures were designed and synthesized in solid phase to demonstrate its application as a scaffold for combinatorial synthesis of coumarins. Thirteen of these derivatives were obtained in high yields. Many of these model compounds fluoresce. Combinatorial libraries constructed with this novel scaffold may have interesting biological or physical properties.

Synthesis of hydrophilic and flexible linkers for peptide derivatization in solid phase.

Four N-Fmoc protected polyoxyethylene-based amino acid type linkers were designed and synthesized for peptide derivatization in solid phase. Three of them were obtained in a crystalline form. The crystallized linkers can be stored at 4 degrees C for 2 years without significant decomposition. Protocols for biotinylation and fluorescent labeling of peptides in solid phase were developed. The linkers also provide good ionization ability for single-bead mass spectrometry analysis of peptides.

Effect of molecular size of pegylated peptide on the pharmacokinetics and tumor targeting in lymphoma-bearing mice.

PURPOSE: Rapid blood and body clearances have hampered effective tumor targeting by small molecules. We used branched poly(ethylene glycol) (pegylated) polymers (M(r) 40,000, M(r) 70,000, M(r) 100,000, and M(r) 150,000) conjugated to tumor-specific and control peptides to assess the effect of both molecular weight and tumor specificity on pharmacokinetics and biodistribution. EXPERIMENTAL DESIGN: Pegylated specific lymphoma-binding peptide and control peptide (containing stereoisomers of proline and aspartate) were synthesized, radiolabeled with (111)In, fractionated by size, and injected into Raji lymphoma-bearing athymic mice (4-6 mice/group). Pharmacokinetics were followed for 2 days to evaluate effects of specificity and molecular size on blood clearance, body clearance, and biodistribution. RESULTS: As molecular size increased, blood and body clearances decreased (P < 0.001). The effect of molecular size on blood clearance was not altered by ligand binding specificity (P = 0.21), with t(1/2) ranging from 5.4 h (M(r) 40,000) to 17.7 h (M(r) 150,000). However, ligand specificity did alter body clearance, with pegylated control peptides clearing the body more slowly than pegylated specific peptides [P = 0.03; range, 19.1-91.3 h (specific peptides) versus 23.6-115.7 h (control peptides)]. At 24 h, there was more uptake of specific versus control pegylated peptides in tumor, liver, and marrow, but there was less uptake in kidneys, with a more pronounced difference for the higher molecular weight peptides (P < 0.01). CONCLUSIONS: These results demonstrate that the pharmacokinetics and biodistribution of peptides and resultant uptake in tumor and normal tissues can be altered by both molecular size and ligand specificity, with molecular size affecting pharmacokinetics and organ uptake in a predictable manner.

High-throughput one-bead-one-compound approach to peptide-encoded combinatorial libraries: MALDI-MS analysis of single TentaGel beads.

The identification of pharmacologically promising compounds (lead compounds) from combinatorial libraries is frequently limited by the throughput of the analytical technique employed. Fourier transform mass spectrometry (FTMS) offers high sensitivity, mass accuracy (m/Deltam > 500 000), and sequencing capabilities. A rapid and efficient method for high-throughput analysis of single beads from peptide-encoded combinatorial libraries with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. Encoding peptides on single beads are identified and structurally characterized by MALDI time-of-flight (TOF) and ultrahigh-resolution MALDI Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. A strategy of on-probe sample preparation is developed to minimize handling of the beads.