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UBQLN1 functions in autophagy and proteasome-mediated protein degradation. It contains an N-terminal ubiquitin-like domain (UBL), a C-terminal ubiquitin-associated domain (UBA), and a flexible central region which functions as a chaperone to prevent protein aggregation. Here, we report the 1H, 15N, and 13C resonance assignments for the backbone (NH, N, C’, Cα, and Hα) and sidechain Cβ atoms of the UBQLN1 UBA and an N-terminally adjacent segment called the UBA-adjacent domain (UBAA). We find a subset of the resonances corresponding to the UBAA to have concentration-dependent chemical shifts, likely due to self-association. We also find the backbone amide nitrogen of T572 to be shifted upfield relative to the average value for a threonine amide nitrogen, a phenomenon likely caused by T572 Hγ1 engagement in a hydrogen bond with adjacent backbone carbonyl atoms. The assignments described in this manuscript can be used to study the protein dynamics of the UBQLN1 UBA and UBAA as well as the interaction of these domains with other proteins.

Supplementary Data from A Phase I Clinical Trial of the Poly(ADP-ribose) Polymerase Inhibitor Veliparib and Weekly Topotecan in Patients with Solid Tumors

Purpose:To determine the dose limiting toxicities (DLT), maximum tolerated dose (MTD), and recommended phase II dose (RP2D) of veliparib in combination with weekly topotecan in patients with solid tumors. Correlative studies were included to assess the impact of topotecan and veliparib on poly(ADP-ribose) levels in peripheral blood mononuclear cells, serum pharmacokinetics of both agents, and potential association of germline repair gene mutations with outcome.Experimental Design:Eligible patients had metastatic nonhematologic malignancies with measurable disease. Using a 3 + 3 design, patients were treated with veliparib orally twice daily on days 1–3, 8–10, and 15–17 and topotecan intravenously on days 2, 9, and 16 every 28 days. Tumor responses were assessed by RECIST.Results:Of 58 patients enrolled, 51 were evaluable for the primary endpoint. The MTD and RP2D was veliparib 300 mg twice daily on days 1–3, 8–10, and 15–17 along with topotecan 3 mg/m2 on days 2, 9, and 16 of a 28-day cycle. DLTs were grade 4 neutropenia lasting >5 days. The median number of cycles was 2 (1–26). The objective response rate was 10%, with 1 complete and 4 partial responses. Twenty-two patients (42%) had stable disease ranging from 4 to 26 cycles. Patients with germline BRCA1, BRCA2, or RAD51D mutations remained on study longer than those without homologous recombination repair (HRR) gene mutations (median 4 vs. 2 cycles).Conclusions:Weekly topotecan in combination with veliparib has a manageable safety profile and appears to warrant further investigation.

Deep eutectic solvents (DESs) have high viscosities, but known to be mitigated by addition of suitable co-solvent. The effect of such co-solvent on the extraction efficiency of the hybrid solvent is hardly known. This study examined the effect of ethanol on three choline chloride-based DESs (glyceline, reline, and ethaline) by mixing each in turn with ethanol in various volume proportions. The hybrid solvents were evaluated for the extraction of benzene from n-hexane. Pseudo-ternary liquid–liquid equilibrium data were obtained using the refractive index method at 303 K and 1 atm for the systems, n-hexane (1) + benzene (2) + hybrid solvent (glyceline/ethanol, ethaline/ethanol, reline/ethanol) (3), and used to evaluate distribution coefficient (D) and selectivity (S). Furthermore, the physicochemical properties of the hybrid solvents were also determined. The results indicate increase in selectivity with increasing ethanol addition up to 50% and decrease with further addition. All hybrid solvents with 50% ethanol outperform sulfolane and are suitable replacement for same as green and sustainable extractant for aromatics from aliphatics. The glyceline + 50% ethanol emerged the overall best with 49.73% elevation in selectivity and 41.15% reduction in viscosity relative to the neat glyceline. The finding of this study is expected to fillip the drive for paradigm shift in petrochemical industries.

The E3 ligase E6AP/UBE3A has a dedicated binding site in the 26S proteasome provided by the RAZUL domain of substrate receptor hRpn10/S5a/PSMD4. Guided by RAZUL sequence similarity, we test and demonstrate here that the E6AP AZUL binds transiently to the UBA of proteasomal shuttle factor UBQLN1/2. Despite a weak binding affinity, E6AP AZUL is recruited to UBQLN2 phase-separated droplets and E6AP interacts with UBQLN1/2 in cells. Steady-state and transfer NOE experiments indicate direct interaction of AZUL with the UBQLN1 UBA domain. Intermolecular contacts identified by NOESY data were combined with AlphaFold2-Multimer predictions to yield an AZUL:UBA model structure. We also identify a concentration-dependent oligomerization domain directly adjacent to UBQLN1/2 UBA (UBA-adjacent, UBAA) that is α-helical and allosterically reconfigured by AZUL binding to UBA. These data lead to a model of E6AP recruitment to UBQLN1/2 by AZUL:UBA interaction and provide fundamental information on binding requirements for interactions in droplets and cells.

A suitable green solvent for extraction of aromatics from aliphatics must possess good solvation and physicochemical properties, a rare occurrence in a single deep eutectic solvent (DES). Mixture of DESs could enable synergy and provide a good candidate extractant. In this study, DESs of glyceline, ethaline, and reline were synthesized and their binary mixtures (glyceline/ethaline, reline/ethaline, and glyceline/reline) produced by blending in various volume proportions. Twelve of such mixed solvents were prepared and their extraction efficiency for separating benzene from n-hexane investigated in a batch equilibrium process. Liquid–liquid equilibria (LLE) data for the pseudo-ternary systems of n-hexane + benzene + mixed DESs were measured at 303 K and 101.3 kPa. The distribution coefficient (D) and selectivity (S) of each pseudo-ternary system were determined to elicit extraction efficiency. The physicochemical properties of the mixed DESs were also measured. The results show that generally the distribution coefficients, selectivities, and physicochemical properties of the mixed DESs lie between the corresponding values for the constituent DES. The best performance was given by the mixed solvent of glyceline and ethaline in the 80:20 volume ratio, respectively, with D = 0.75 and S = 422.485. This assertion was further corroborated by higher percent recovery of benzene obtained from the said mixed DES (57.88%) relative to other mixed DESs (≤ 49.11%) examined in this study. Furthermore, its separation efficiency is superior to sulfolane but lower than glyceline, though there was a 9.4% reduction in its viscosity relative to glyceline.

Waste tyre pyrolysis gasoline (WTPG) contain significant amount of aromatics such as benzene, toluene and xylenes (BTX) and thus provide a good source for these value-added chemicals. Separation of aromatics from aliphatic media as obtained in WTPG and naphtha is done commercially by solvent extraction using volatile organic solvents such as sulfolane (SUF), dimethylformamide (DMF) and diethylene glycol (DEG). The high cost of this state-of-the art separation method and environmental consideration have necessitated search for non-volatile and green solvent such as deep eutectic solvent (DES). This study intends to conduct a comparative evaluation of the performance of five solvents (SUF, DMF, DEG, and two DESs) for the extraction of BTX from WTPG. The two DESs are choline chloride/ethylene glycol (DES1) and choline chloride/glycerol (DES2) in molar ratios 1:2. An ASPEN plus simulation was carried out to generate liquid–liquid equilibria (LLE) data for the pseudo-ternary systems {WTPG + BTX + solvent (SUF/DMF/DEG/DES)}. Performance evaluation was based on selectivity (S) and solute (BTX) distribution coefficient (D). The propriety of the simulation protocol was validated using literature data. The results revealed the following maximum values of selectivity and distribution coefficients for the solvents: DES2 (S = 378.283, D = 0.656); DES1 (S = 77.364, D = 1.423); SUF (S = 55.371, D = 0.756); DMF (S = 25.336, D = 0.786) and DEG (S = 17.531, D = 0.793). The DESs therefore performed better than the organic solvents and can suitably replace same in the extraction of BTX from waste tyre pyrolysis gasoline.

In this study, deep eutectic solvents (DESs) were prepared using choline chloride as hydrogen bond acceptor (HBA) and ethylene glycol (EG) or glycerol (GLY) or urea (U) as hydrogen bond donor (HBD) and were evaluated as solvents in the extraction of benzene from n-hexane. Six of such solvents were prepared using different molar ratios of HBA: HBD and code named DES1, DES2, DES3, DES4, DES5 and DES6. Liquid–liquid equilibria (LLE) data for the ternary systems of n-hexane-benzene-DESs were measured at 303 K and 101.3 kPa. Solubility data and mutual solubilities between n-hexane and DES were measured using the traditional cloud point method. The tie lines were obtained using titration and refractive index measurements on both phases (n-hexane phase and DES-phases). The ternary systems exhibit type-1 phase behavior. The Othmer-Tobias and Hands equations were applied to examine the reliability of the LLE data. The tie-line data were correlated using the nonrandom two-liquid (NRTL) and universal quasichemical (UNIQUAC) thermodynamic models, and their corresponding binary interaction parameters were determined. The results show that the maximum separation factors were 31.24, 462.00, 15.24, 37.83, 174.60 and 126.00 for DES1, DES2, DES3, DES4, DES5 and DES6, respectively. The glycerol based DES (DES2 and DES5) show the highest separation factors and thus considered the most suitable for separating benzene from hexane. The regression coefficient for both Othmer-Tobias and Hand equations are higher than 0.99 for all DESs, indicating the reliability and consistency of the data. Both NRTL and UNIQUAC models adequately capture the experimental data.

The authors aim to develop siRNA therapeutics for cancer that can be administered systemically to target tumors and retard their growth. The efficacy of systemic delivery of siRNA to tumors with nanoparticles based on lipids or polymers is often compromised by their rapid clearance from the circulation by the liver. Here, multifunctional cationic and anionic siRNA nanoparticle formulations are described, termed receptor-targeted nanocomplexes (RTNs), that comprise peptides for siRNA packaging into nanoparticles and receptor-mediated cell uptake, together with lipids that confer nanoparticles with stealth properties to enhance stability in the circulation, and fusogenic properties to enhance endosomal release within the cell. Intravenous administration of RTNs in mice leads to predominant accumulation in xenograft tumors, with very little detected in the liver, lung, or spleen. Although non-targeted RTNs also enter the tumor, cell uptake appears to be RGD peptide-dependent indicating integrin-mediated uptake. RTNs with siRNA against

Deep eutectic solvents (DESs) have high viscosities, but known to be mitigated by addition of suitable co-solvent. The effect of such co-solvent on the extraction efficiency of the hybrid solvent is hardly known. This study examined the effect of ethanol on three choline chloride-based DESs (glyceline, reline, and ethaline) by mixing each in turn with ethanol in various volume proportions. The hybrid solvents were evaluated for the extraction of benzene from n-hexane. Pseudo-ternary liquid–liquid equilibrium data were obtained using the refractive index method at 303 K and 1 atm for the systems, n-hexane (1) + benzene (2) + hybrid solvent (glyceline/ethanol, ethaline/ethanol, reline/ethanol) (3), and used to evaluate distribution coefficient (D) and selectivity (S). Furthermore, the physicochemical properties of the hybrid solvents were also determined. The results indicate increase in selectivity with increasing ethanol addition up to 50% and decrease with further addition. All hybrid solvents with 50% ethanol outperform sulfolane and are suitable replacement for same as green and sustainable extractant for aromatics from aliphatics. The glyceline + 50% ethanol emerged the overall best with 49.73% elevation in selectivity and 41.15% reduction in viscosity relative to the neat glyceline. The finding of this study is expected to fillip the drive for paradigm shift in petrochemical industries. Supplementary Information The online version contains supplementary material available at 10.1007/s13203-021-00282-y.

Performance monitoring and state estimation are promising techniques to ensure high reliability in Internet of Things (IoT). A major data-driven approach that addresses the decentralized and heterogeneous nature of IoT is distributed computing. Values from physical measurements and temporal dimension in transmitted sensor data can be analyzed in a distributed manner for state estimation. In this paper, we discuss a smart home energy utilization problem and the effects of climatic conditions. We focus on determining patterns, correlations and predicting weather attributes in a distributed and scalable manner using Message Passing Interface (MPI). Our results show that our distributed approach is scalable up to 24 nodes or processes, which can further scale up to 1000 nodes or processes depending on the number of indivisible subtasks that need to be computed. We also compare the execution time for the distributed tasks and notice a performance gain due to parallelization. Furthermore, we develop a model based on Long Short-Term Memory (LSTM) to estimate the expected energy to be utilized in a smart home environment. We evaluate our work using an IoT dataset to show the effectiveness of our approach.

Substitution of the m,p-chloro groups of bis-benzylidinepiperidone RA190 for p-nitro, generating RA183, enhanced covalent drug binding to Cys88 of RPN13. Treatment of cancer cell lines with RA183 inhibited ubiquitin-mediated protein degradation, resulting in rapid accumulation of high-molecular-weight polyubiquitinated proteins, blockade of NFκB signaling, endoplasmic reticulum stress, an unfolded protein response, production of reactive oxygen species, and apoptotic cell death. High-grade ovarian cancer, triple-negative breast cancer, and multiple myeloma cell lines were particularly vulnerable to RA183. RA183 stabilized a tetraubiquitin-linked firefly luciferase reporter protein in cancer cell lines and mice, demonstrating in vitro and in vivo proteasomal inhibition, respectively. However, RA183 was rapidly cleared from plasma, likely reflecting its rapid degradation to the active compound RA9, as seen in human liver microsomes. Intraperitoneal administration of RA183 inhibited proteasome function and orthotopic tumor growth in mice bearing human ovarian cancer model ES2-luc ascites or syngeneic ID8-luc tumor.

In this current era of Internet of Things, data privacy and security of internet enabled devices has become a major concern of many users and manufacturers. Massive amount of data is being generated by these IoT devices and there might be possibilities of user's information being exposed without any privacy protection. The rate of data transfer, size, kind of information transmitted and secure channels used by these IoT devices are of utmost importance and demand more exploratory research. It is not all IoT devices that utilize encryption in their data transmission and those devices that incorporate such security measure can be compromised by the interception of generated traffic via proxy server and its decryption. In this paper, we explore and investigate the data being transmitted by six representative IoT devices and analyze the data, using a proxy server to capture both HTTP and HTTPS traffic. Our results show that one of the IoT devices transmit data in plain text while others utilize encryption. User's information, MAC address and IP address were identified in our data analysis. We propose that IoT devices should not allow proxy connections and implement machine learning algorithms to detect proxies using network connection information.

PURPOSE: The purpose of this report is to describe, for the first time, the pharmacokinetics of dacarbazine (DTIC) and its metabolites (5-[3-methyl-triazen-1-yl]-imidazole-4-carboxamide (MTIC), 5-[3-hydroxymethyl-3-methyl-triazen-1-yl]-imidazole-4-carboxamide (HMMTIC) and 5-aminoimidazole-4-carboxamide (AIC)) during pregnancy (n=2) and postpartum (n=1). METHODS: Non-compartmental DTIC, MTIC, HMMTIC and AIC pharmacokinetics (PK) were estimated in one case at 29 weeks gestation and 18 days postpartum and a second case at 32 weeks gestation, in women receiving DTIC in combination with doxorubicin, bleomycin and vinblastine for treatment of Hodgkin’s Lymphoma. Drug concentrations were measured by HPLC. RESULTS: In the subject who completed both pregnancy and postpartum study days, DTIC area under the concentration-time curve (AUC) was 27% higher and metabolite AUCs were lower by 27% for HMMTIC, 38% for MTIC and 83% of AIC during pregnancy compared to postpartum. At 7 and 9 years follow-up, both subjects were in remission of their Hodgkin’s Lymphoma. CONCLUSIONS: Based on these two case reports, pregnancy appears to decrease the metabolism of the pro-drug dacarbazine, likely through inhibition of CYP1A2 activity. Lower concentrations of active metabolites and decreased efficacy may result, although both of these subjects experienced long-term remission of their Hodgkin’s Lymphoma.

Human mesotrypsin is highly homologous to other mammalian trypsins, and yet it is functionally unique in possessing resistance to inhibition by canonical serine protease inhibitors and in cleaving these inhibitors as preferred substrates. Arg-193 and Ser-39 have been identified as contributors to the inhibitor resistance and cleavage capability of mesotrypsin, but it is not known whether these residues fully account for the unusual properties of mesotrypsin. Here, we use human cationic trypsin as a template for engineering a gain of catalytic function, assessing mutants containing mesotrypsin-like mutations for resistance to inhibition by bovine pancreatic trypsin inhibitor (BPTI) and amyloid precursor protein Kunitz protease inhibitor (APPI), and for the ability to hydrolyze these inhibitors as substrates. We find that Arg-193 and Ser-39 are sufficient to confer mesotrypsin-like resistance to inhibition; however, compared with mesotrypsin, the trypsin-Y39S/G193R double mutant remains 10-fold slower at hydrolyzing BPTI and 2.5-fold slower at hydrolyzing APPI. We identify two additional residues in mesotrypsin, Lys-74 and Asp-97, which in concert with Arg-193 and Ser-39 confer the full catalytic capability of mesotrypsin for proteolysis of BPTI and APPI. Novel crystal structures of trypsin mutants in complex with BPTI suggest that these four residues function cooperatively to favor conformational dynamics that assist in dissociation of cleaved inhibitors. Our results reveal that efficient inhibitor cleavage is a complex capability to which at least four spatially separated residues of mesotrypsin contribute. These findings suggest that inhibitor cleavage represents a functional adaptation of mesotrypsin that may have evolved in response to positive selection pressure.

Purpose: To determine the dose limiting toxicities (DLT), maximum tolerated dose (MTD), and recommended phase II dose (RP2D) of veliparib in combination with weekly topotecan in patients with solid tumors. Correlative studies were included to assess the impact of topotecan and veliparib on poly(ADP-ribose) levels in peripheral blood mononuclear cells, serum pharmacokinetics of both agents, and potential association of germline repair gene mutations with outcome. Experimental Design: Eligible patients had metastatic nonhematologic malignancies with measurable disease. Using a 3 + 3 design, patients were treated with veliparib orally twice daily on days 1–3, 8–10, and 15–17 and topotecan intravenously on days 2, 9, and 16 every 28 days. Tumor responses were assessed by RECIST. Results: Of 58 patients enrolled, 51 were evaluable for the primary endpoint. The MTD and RP2D was veliparib 300 mg twice daily on days 1–3, 8–10, and 15–17 along with topotecan 3 mg/m2 on days 2, 9, and 16 of a 28-day cycle. DLTs were grade 4 neutropenia lasting >5 days. The median number of cycles was 2 (1–26). The objective response rate was 10%, with 1 complete and 4 partial responses. Twenty-two patients (42%) had stable disease ranging from 4 to 26 cycles. Patients with germline BRCA1, BRCA2, or RAD51D mutations remained on study longer than those without homologous recombination repair (HRR) gene mutations (median 4 vs. 2 cycles). Conclusions: Weekly topotecan in combination with veliparib has a manageable safety profile and appears to warrant further investigation.

PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pathological role of this enzyme, and could potentially form the basis for novel therapeutic strategies targeting mesotrypsin. A virtual screen of the Natural Product Database (NPD) and Food and Drug Administration (FDA) approved Drug Database was conducted by high-throughput molecular docking utilizing crystal structures of mesotrypsin. Twelve high-scoring compounds were selected for testing based on lowest free energy docking scores, interaction with key mesotrypsin active site residues, and commercial availability. Diminazene (CID22956468), along with two similar compounds presenting the bis-benzamidine substructure, was validated as a competitive inhibitor of mesotrypsin and other human trypsin isoforms. Diminazene is the most potent small molecule inhibitor of mesotrypsin reported to date with an inhibitory constant (Ki) of 3.6±0.3 μM. Diminazene was subsequently co-crystalized with mesotrypsin and the crystal structure was solved and refined to 1.25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures.

Engineered protein therapeutics offer advantages, including strong target affinity, selectivity and low toxicity, but like natural proteins can be susceptible to proteolytic degradation, thereby limiting their effectiveness. A compelling therapeutic target is mesotrypsin, a protease up-regulated with tumour progression, associated with poor prognosis, and implicated in tumour growth and progression of many cancers. However, with its unique capability for cleavage and inactivation of proteinaceous inhibitors, mesotrypsin presents a formidable challenge to the development of biological inhibitors. We used a powerful yeast display platform for directed evolution, employing a novel multi-modal library screening strategy, to engineer the human amyloid precursor protein Kunitz protease inhibitor domain (APPI) simultaneously for increased proteolytic stability, stronger binding affinity and improved selectivity for mesotrypsin inhibition. We identified a triple mutant APPIM17G/I18F/F34V, with a mesotrypsin inhibition constant (Ki) of 89 pM, as the strongest mesotrypsin inhibitor yet reported; this variant displays 1459-fold improved affinity, up to 350 000-fold greater specificity and 83-fold improved proteolytic stability compared with wild-type APPI. We demonstrated that APPIM17G/I18F/F34V acts as a functional inhibitor in cell-based models of mesotrypsin-dependent prostate cancer cellular invasiveness. Additionally, by solving the crystal structure of the APPIM17G/I18F/F34V–mesotrypsin complex, we obtained new insights into the structural and mechanistic basis for improved binding and proteolytic resistance. Our study identifies a promising mesotrypsin inhibitor as a starting point for development of anticancer protein therapeutics and establishes proof-of-principle for a novel library screening approach that will be widely applicable for simultaneously evolving proteolytic stability in tandem with desired functionality for diverse protein scaffolds.