Kinetic Study of the Esterase-like Activity of Albumin following Condensation by Macromolecular Crowding.

The ability of bovine serum albumin (BSA) to form condensates in crowded environments has been discovered only recently. Effects of this condensed state on the secondary structure of the protein have already been unraveled as some aging aspects, but the pseudo-enzymatic behavior of condensed BSA has never been reported yet. This article investigates the kinetic profile of para-nitrophenol acetate hydrolysis by BSA in its condensed state with poly(ethylene) glycol (PEG) as the crowding agent. Furthermore, the initial BSA concentration was varied between 0.25 and 1 mM which allowed us to modify the size distribution, the volume fraction, and the partition coefficient (varying from 136 to 180). Hence, the amount of BSA originally added was a simple way to modulate the size and density of the condensates. Compared with dilute BSA, the initial velocity (vi) with condensates was dramatically reduced. From the Michaelis-Menten fits, the extracted Michaelis constant Km and the maximum velocity Vmax decreased in control samples without condensates when the BSA concentration increased, which was attributed to BSA self-oligomerization. In samples containing condensates, the observed vi was interpreted as an effect of diluted BSA remaining in the supernatants and from the condensates. In supernatants, the crowding effect of PEG increased the kcat and catalytic efficiency. Last, Vmax was proportional to the volume fraction of the condensates, which could be controlled by varying its initial concentration. Hence, the major significance of this article is the control of the size and volume fraction of albumin condensates, along with their kinetic profile using liquid-liquid phase separation.

Co(II) Substitution Enhances the Esterase Activity of a de Novo Designed Zn(II) Carbonic Anhydrase.

Carbonic Anhydrases (CAs) have been a target for de novo protein designers due to the simplicity of the active site and rapid rate of the reaction. The first reported mimic contained a Zn(II) bound to three histidine imidazole nitrogens and an exogenous water molecule, hence closely mimicking the native enzymes' first coordination sphere. Co(II) has served as an alternative metal to interrogate CAs due to its d7 electronic configuration for more detailed solution characterization. We present here the Co(II) substituted [Co(II)(H2O/OH-)]N(TRIL2WL23H)3 n+ that behaves similarly to native Co(II) substituted human-CAs. Like the Zn(II) analogue, the cobalt-derivative at slightly basic pH is incapable of hydrolyzing p-nitrophenylacetate (pNPA); however, as the pH is increased a significant activity develops, which at pH values above 10 eventually yields a catalytic efficiency that exceeds that of the [Zn(II)(OH-)]N(TRIL2WL23H)3 + peptide complex. X-ray absorption analysis is consistent with an octahedral species at pH 7.5 that converts to a 5-coordinate species by pH 11. UV-vis spectroscopy can monitor this transition, giving a pKa for the conversion of 10.3. We assign this conversion to the formation of a 5-coordinate Co(II)(Nimid)3(OH)(H2O) species. The pH dependent kinetic analysis indicates the maximal rate (kcat), and thus the catalytic efficiency (kcat/Km), follow the same pH profile as the spectroscopic conversion to the pentacoordinate species. This correlation suggests that the chemically irreversible ester hydrolysis corresponds to the rate determining process.

A meta-analysis of methane-mitigation potential of feed additives evaluated in vitro.

A systematic literature review of in vitro studies was performed to identify methane (CH4) mitigation interventions with a potential to reduce CH4 emission in vivo. Data from 277 peer-reviewed studies published between 1979 and 2018 were reviewed. Individual CH4 mitigation interventions were classified into 14 categories of feed additives based on their type, chemical composition, and mode of action. Response variables evaluated were absolute CH4 emission (number of treatment means comparisons = 1,325); total volatile fatty acids (n = 1,007), acetate (n = 783), propionate (n = 792), and butyrate (n = 776) concentrations; acetate to propionate ratio (n = 675); digestibility of dry matter (n = 489), organic matter (n = 277), and neutral detergent fiber (n = 177). Total gas production was used as an explanatory variable in the model for CH4 production. Relative mean difference between treatment and control means reported in the studies was calculated and used for statistical analysis. The robust variance estimation method was used to analyze the effects of CH4 mitigation interventions. In vitro CH4 production was decreased by antibodies (-38.9%), chemical inhibitors (-29.2%), electron sinks (-18.9%), essential oils (-18.2%), plant extracts (-14.5%), plant inclusion (-11.7%), saponins (-14.8%), and tannins (-14.5%). Overall effects of direct-fed microbials, enzymes, macroalgae, and organic acids supplementation did not affect CH4 production in the current meta-analysis. When considering the effects of individual mitigation interventions containing a minimum number of 4 degrees of freedom within feed additives categories, Enterococcus spp. (i.e., direct-fed microbial), nitrophenol (i.e., electron sink), and Leucaena spp. (i.e., tannins) decreased CH4 production by 20.3%, 27.1%, and 23.5%, respectively, without extensively, or only slightly, affecting ruminal fermentation and digestibility of nutrients. It should be noted, however, that although the total number of publications (n = 277) and treatment means comparisons (n = 1,325 for CH4 production) in the current analysis were high, data for most mitigation interventions were obtained from less than 5 observations (e.g., maximum number of observations was 4, 7, and 22 for nitrophenol, Enterococcus spp., and Leucaena spp., respectively), because of limited data available in the literature. These should be further evaluated in vitro and in vivo to determine their true potential to decrease enteric CH4 production, yield, and intensity. Some mitigation interventions (e.g., magnesium, Heracleum spp., nitroglycerin, ß-cyclodextrin, Leptospermum pattersoni, Fructulus Ligustri, Salix caprea, and Sesbania grandiflora) decreased in vitro CH4 production by over 50% but did not have enough observations in the database. These should be more extensively investigated in vitro, and the dose effect must be considered before adoption of mitigation interventions in vivo.

Nitrophenols disrupt the expression and activity of biotransformation enzymes (CYP3A and COMT) in chicken ovarian follicles in vivo and in vitro.

Nitrophenols are environmental pollutants and xenobiotics, the main sources of which are diesel exhaust fumes and pesticides. The biotransformation processes that take place in the liver are defence mechanisms against xenobiotics, such as nitrophenols. Our previous study showed that the chicken ovary is an additional xenobiotic detoxification place and that nitrophenols disrupt steroidogenesis in chicken ovarian follicles. Therefore, the present study aimed to determine the in vivo and in vitro effects of 4-nitrophenol (PNP) and 3-methyl-4-nitrophenol (PNMC) on the expression and activity of phase I (CYP3A) and phase II (COMT) biotransformation enzymes in chicken ovary. In an in vivo study, hens were treated with a vehicle or 10 mg PNP or PNMC/kg b.wt. per day for 6 days. In an in vitro study, prehierarchical white and yellowish follicles, as well as the granulosa and theca layers of the three largest preovulatory follicles (F3, F2 and F1), were isolated and then incubated in a control medium or medium supplemented with PNP (10-6 M) or PNMC (10-6 M) for 24 or 48 h. Both in vivo and in vitro studies showed that nitrophenols exert tissue- and compound-dependent (PNP or PNMC) effects on CYP3A and COMT gene (real-time PCR) protein (Western blot) expression and their activity (colorimetric methods). The inhibitory effect of nitrophenols in vivo on the activity of biotransformation enzymes suggest that the ovary has the capacity to metabolise PNP and PNMC.

Platinum-Based Mcl-1 Inhibitor Targeting Mitochondria Achieves Enhanced Antitumor Activity as a Single Agent or in Combination with ABT-199.

Discovery of small molecule inhibitors targeting Mcl-1 (Myeloid cell leukemia 1) confronts many challenges. Based on the fact that Mcl-1 is mainly localized in mitochondria, we propose a new strategy of targeting mitochondria to improve the binding efficiency of Mcl-1 inhibitors. We report the discovery of complex 9, the first mitochondrial targeting platinum-based inhibitor of Mcl-1, which selectively binds to Mcl-1 with high binding affinity. Complex 9 was mainly concentrated in the mitochondria of tumor cells which led to an enhanced antitumor efficacy. Complex 9 induced Bax/Bak-dependent apoptosis in LP-1 cells and synergized with ABT-199 to kill ABT-199 resistant cells in multiple cancer models. Complex 9 was effective and tolerable as a single agent or in combination with ABT-199 in mouse models. This research work demonstrated that developing mitochondria-targeting Mcl-1 inhibitors is a new potentially efficient strategy for tumor therapy.

Sequentially modified carbon felt for enhanced p-nitrophenol biodegradation through direct interspecific electron transfer.

The widely applied aromatic nitration in modern industry leads to toxic p-nitrophenol (PNP) in environment. Exploring its efficient degradation routes is of great interests. In this study, a novel four-step sequential modification procedure was developed to increase the specific surface area, functional group, hydrophilicity, and conductivity of carbon felt (CF). The implementation of the modified CF promoted reductive PNP biodegradation, attaining 95.2 ± 0.8% of removal efficiency with less accumulation of highly toxic organic intermediates (e.g., p-aminophenol), compared to carrier-free and CF-packed biosystems. The constructed anaerobic-aerobic process with modified CF in 219-d continuous operation achieved further removal of carbon and nitrogen containing intermediates and partial mineralization of PNP. The modified CF promoted the secretion of extracellular polymeric substances (EPS) and cytochrome c (Cyt c), which were essential components to facilitate direct interspecies electron transfer (DIET). Synergistic relationship was deduced that glucose was converted into volatile fatty acids by fermenters (e.g., Longilinea and Syntrophobacter), which donated electrons to the PNP degraders (e.g., Bacteroidetes_vadinHA17) through DIET channels (CF, Cyt c, EPS) to complete PNP removal. This study proposes a novel strategy using engineered conductive material to enhance the DIET process for efficient and sustainable PNP bioremediation.

The environmental pollutant 3-methyl-4-nitrophenol reduces the regulatory T cells in the intestine.

Dysfunction of immune regulation plays a crucial role in the pathogenesis of many immune disorders in the body. The underlying mechanism is still not completely understood. Environmental pollution contributes to immune de-regulation. 3-methyl-4-nitrophenol (MNP) is one of the major environmental pollutants. This study aims to investigate the role of MNP in compromising immune regulatory functions in the intestine. A food allergy (FA) mouse model was established using ovalbumin (OVA) as the specific antigen. The activities of regulatory T cells in the mouse intestine were evaluated by flow cytometry and enzyme-linked immunosorbent assay. We found that MNP reduced the CD4+ Foxp3+ Treg frequency, increased Th17 cells, and converted Tregs to Th17 cells in the intestine. MNP induced the expression of IL-6 in regulatory T cells (Tregs). Estrogen receptor (ER) mediated the effects of MNP on promoting IL-6 expression in Tregs. The IL-6 in synergy with transforming growth factor (TGF)-ß to convert Tregs to Th17 cells. The concomitant exposure of MNP and OVA induced FA like response in mice. Modulation of the ER-STAT3-IL-6 signal pathway attenuated mouse FA response. In summary, MNP, an environmental pollutant, acts as an immunoadjuvant for developing FA. By activation of the estrogen receptor, MNP induces Tregs to express IL-6. IL-6 in synergy with TGF-ß converts Tregs to Th17 cells.

Isolation and test of novel yeast strains with lignin usage capability and phenolic compound resistance.

Five yeast fungi strains (i.e., two Cryptococcus albidus, one Candida guillermondii, and two Candida tropicalis) were isolated from sugarcane and tested for their use of lignin as sole carbon source and their potential to grow in the presence of phenol and phenol derivatives (i.e., pentachlorophenol and p-nitrophenol). The full set of isolated yeasts showed ligninolytic activity, achieving at least 36% lignin degradation after 25 days. The C. albidus JS-B1 strain had the highest ligninolytic activity, achieving 27% lignin degradation within 4 days. This increased activity was associated with the production of ligninolytic laccase enzymes. All the tested yeast fungi strains showed growth in the presence of high concentrations of phenolic compounds (i.e., 900 mg/L phenol, 200 mg/L p-nitrophenol, 50 mg/L pentachlorophenol) and showed significant potential for lignin and lignin by-product degradation. Each of these five strains has the potential to be used in biological treatment processes for contaminated effluents from paper pulping and bleaching or phenol and phenol-derivative biodegradation processes for other industrial wastewater effluents.

Cytotoxicity and oxidative stress induced by atmospheric mono-nitrophenols in human lung cells.

Nitrophenols (NPs) are hazardous pollutants found in various environmental matrices, including ambient fine particulate matter (PM2.5), agricultural residues, rainwater, wildfires, and industrial wastes. This study showed for the first time the effect of three pure nitrophenols and their mixture on human lung cells to provide basic understanding of the NP influence on cell elements and processes. We identified NPs in ambient PM2.5 and secondary organic aerosol (SOA) particles generated from the photooxidation of monocyclic aromatic hydrocarbons in the U.S. EPA smog chamber. We assessed the toxicity of identified NPs and their equimolar mixture in normal bronchial epithelial (BEAS-2B) and alveolar epithelial cancer (A549) lung cell lines. The inhibitory concentration-50 (IC50) values were highest and lowest in BEAS-2B cells treated with 2-nitrophenol (2NP) and 4-nitrophenol (4NP), respectively, at 24 h of exposure. The lactate dehydrogenase (LDH) assay showed that 4NP, the most abundant NP we identified in PM2.5, was the most cytotoxic NP examined in both cell lines. The annexin-V/fluorescein isothiocyanate (FITC) analysis showed that the populations of late apoptotic/necrotic BEAS-2B and A549 cells exposed to 3NP, 4NP, and NP equimolar mixture increased between 24 and 48 h. Cellular reactive oxygen species (ROS) buildup led to cellular death post exposure to 3NP, 4NP and the NP mixtures, while 2NP induced the lowest ROS buildup. An increased mitochondrial ROS signal following NP exposure occurred only in BEAS-2B cells. The tetramethylrhodamine, methyl ester, perchlorate (TMRM) assay showed that exposed cells exhibited collapse of the mitochondrial membrane potential. TMRM signals decreased significantly only in BEAS-2B cells, and most strongly with 4NP exposures. Our results suggest that acute atmospheric exposures to NPs may be toxic at high concentrations, but not at ambient PM2.5 concentrations. Further chronic studies with NP and NP-containing PM2.5 are warranted to assess their contribution to lung pathologies.

Iron carriers promote biofilm formation and p-nitrophenol degradation.

Vertical baffled biofilm reactors (VBBR) equipped with Plastic-carriers and Fe-carriers were employed to explore the effect of biofilm carriers on biofilm formation and p-nitrophenol (PNP) degradation. The results showed that Fe-carriers enhanced biofilm formation and PNP degradation. The maximum thickness of biofilm grown on the Fe-carriers was 1.5-fold higher than that on the Plastic-carriers. The Fe-VBBR reached a maximum rate of PNP removal at 13.02 µM L-1 h-1 with less sodium acetate addition (3 mM), while the maximum rate of PNP removal was 11.53 µM L-1 h-1 with more sodium acetate addition (6 mM) in the Plastic-based VBBR. High-throughput sequencing suggested that the Fe-VBBR had a higher biodiversity of the bacterial community in evenness, and the Achromobacter genus and Xanthobacteraceae family were as main PNP degraders. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology analysis suggested more abundances of iron uptake genes were expressed to transport iron into the cytoplasm under an iron-limited condition in two VBBRs, and the metabolic pathway of PNP degradation went through 4-nitrocatechol and 1,2,4-benzenetriol. Our results provide a new insight for iron enhancing biofilm formation and PNP degradation.

The catalytic and ROS-scavenging activities of green synthesized, antiferromagneticα-Fe2O3nanoparticle with a prismatic octahedron morphology from pomegranate rind extract.

Phenolic compounds (like 4-nitrophenol) and dyes (like methyl orange) are common by-products discharged by many industries as wastes; they are toxic and may induce discomfort and irritation in humans when ingested. Most of these compounds can be made less toxic through catalytic degradation. Metal oxide nanoparticles are found to have high catalytic activity and can degrade toxic phenolic compounds and dyes. In the current study, pomegranate rind extract was used for the green synthesis of iron oxide nanoparticles that exhibited an octahedron morphology revealed by scanning electron microscopy analysis. Energy dispersive x-ray analysis showed 47.96% content of Fe (by weight); high resolution-transmission electron microscopy analysis confirmed that the nanoparticles had a particle size of 22.54 ± 4.13 nm. The particles were further characterized by x-ray diffraction, fourier transform-infrared spectroscopy, vibrating sample magnetometer, and thermogravimetric analysis. The nanoparticle proved to be efficient in reducing 4-nitrophenol and methyl orange. It was also found to be non-toxic towards murine macrophages, RAW 264.7 with good ROS-scavenging potential compared to control.

Esterase Activity of Serum Albumin Studied by 1H NMR Spectroscopy and Molecular Modelling.

Serum albumin possesses esterase and pseudo-esterase activities towards a number of endogenous and exogenous substrates, but the mechanism of interaction of various esters and other compounds with albumin is still unclear. In the present study, proton nuclear magnetic resonance (1H NMR) has been applied to the study of true esterase activity of albumin, using the example of bovine serum albumin (BSA) and p-nitrophenyl acetate (NPA). The site of BSA esterase activity was then determined using molecular modelling methods. According to the data obtained, the accumulation of acetate in the presence of BSA in the reaction mixture is much more intense as compared with the spontaneous hydrolysis of NPA, which indicates true esterase activity of albumin towards NPA. Similar results were obtained for p-nitophenyl propionate (NPP) as substrate. The rate of acetate and propionate release confirms the assumption that there is a site of true esterase activity in the albumin molecule, which is different from the site of the pseudo-esterase activity Sudlow II. The results of molecular modelling of BSA and NPA interaction make it possible to postulate that Sudlow site I is the site of true esterase activity of albumin.

Single-Component and Two-Component para-Nitrophenol Monooxygenases: Structural Basis for Their Catalytic Difference.

para-Nitrophenol (PNP) is a hydrolytic product of organophosphate insecticides, such as parathion and methylparathion, in soil. Aerobic microbial degradation of PNP has been classically shown to proceed via the "hydroquinone (HQ) pathway" in Gram-negative degraders, whereas it proceeds via the "benzenetriol (BT) pathway" in Gram-positive ones. The "HQ pathway" is initiated by a single-component PNP 4-monooxygenase and the "BT pathway" by a two-component PNP 2-monooxygenase. Their regioselectivity intrigued us enough to investigate their catalytic difference through structural study. PnpA1 is the oxygenase component of the two-component PNP 2-monooxygenase from Gram-positive Rhodococcus imtechensis strain RKJ300. It also catalyzes the hydroxylation of 4-nitrocatechol (4NC) and 2-chloro-4-nitrophenol (2C4NP). However, the mechanisms are unknown. Here, PnpA1 was structurally determined to be a member of the group D flavin-dependent monooxygenases with an acyl coenzyme A (acyl-CoA) dehydrogenase fold. The crystal structure and site-directed mutagenesis underlined the direct involvement of Arg100 and His293 in catalysis. The bulky side chain of Val292 was proposed to push the substrate toward flavin adenine dinucleotide (FAD), hence positioning the substrate properly. An N450A variant was found with improved activity for 4NC and 2C4NP-probably because of the reduced steric hindrance. PnpA1 shows an obvious difference in substrate selectivity with its close homologues TcpA and TftD, which may be caused by the unique Thr296 and a different conformation in the loop from positions 449 to 454 (loop 449-454). Above all, our study allows structural comparison between the two types of PNP monooxygenases. An explanation that accounts for their regioselectivity was proposed: the different PNP binding manners determine their choice of ortho- or para-hydroxylation on PNP. IMPORTANCE Single-component PNP monoxygenases hydroxylate PNP at the 4 position, while two-component ones do so at the 2 position. However, their catalytic and structural differences remain elusive. The structure of single-component PNP 4-monooxygenase has previously been determined. In this study, to illustrate their catalytic difference, we resolved the crystal structure of PnpA1, a typical two-component PNP 2-monooxygenase. The roles of several key amino acid residues in substrate binding and catalysis were revealed, and a variant with improved activities toward 4NC and 2C4NP was obtained. Moreover, through comparison of the two types of PNP monooxygenases, a hypothesis was proposed to account for their catalytic difference, which gives us a better understanding of these two similar reactions at the molecular level. In addition, these results will also be of further aid in rational design of enzymes in bioremediation and biosynthesis.

Effects of genetic polymorphisms on the sulfation of doxorubicin by human SULT1C4 allozymes.

Doxorubicin is a chemotherapeutic drug widely utilized in cancer treatment. An enzyme critical to doxorubicin metabolism is the cytosolic sulfotransferase (SULT) SULT1C4. This study investigated the functional impact of SULT1C4 single nucleotide polymorphisms (SNPs) on the sulfation of doxorubicin by SULT1C4 allozymes. A comprehensive database search was performed to identify various SULT1C4 SNPs. Ten nonsynonymous SULT1C4 SNPs were selected, and the corresponding cDNAs, packaged in pGEX-2TK expression vector, were generated via site-directed mutagenesis. Respective SULT1C4 allozymes were bacterially expressed and purified by affinity chromatography. Purified SULT1C4 allozymes, in comparison with the wild-type enzyme, were analysed for sulphating activities towards doxorubicin and 4-nitrophenol, a prototype substrate. Results obtained showed clearly differential doxorubicin-sulphating activity of SULT1C4 allozymes, implying differential metabolism of doxorubicin through sulfation in individuals with distinct SULT1C4 genotypes.

Structural basis for transglycosylation in glycoside hydrolase family GH116 glycosynthases.

Glycosynthases are glycoside hydrolase mutants that can synthesize oligosaccharides or glycosides from an inverted donor without hydrolysis of the products. Although glycosynthases have been characterized from a variety of glycoside hydrolase (GH) families, family GH116 glycosynthases have yet to be reported. We produced the Thermoanaerobacterium xylanolyticum TxGH116 nucleophile mutants E441D, E441G, E441Q and E441S and compared their glycosynthase activities to the previously generated E441A mutant. The TxGH116 E441G and E441S mutants exhibited highest glycosynthase activity to transfer glucose from α-fluoroglucoside (α-GlcF) to cellobiose acceptor, while E441D had low but significant activity as well. The E441G, E441S and E441A variants showed broad specificity for α-glycosyl fluoride donors and p-nitrophenyl glycoside acceptors. The structure of the TxGH116 E441A mutant with α-GlcF provided the donor substrate complex, while soaking of the TxGH116 E441G mutant with α-GlcF resulted in cellooligosaccharides extending from the +1 subsite out of the active site, with glycerol in the -1 subsite. Soaking of E441A or E441G with cellobiose or cellotriose gave similar acceptor substrate complexes with the nonreducing glucosyl residue in the +1 subsite. Combining structures with the ligands from the TxGH116 E441A with α-GlcF crystals with that of E441A or E441G with cellobiose provides a plausible structure of the catalytic ternary complex, which places the nonreducing glucosyl residue O4 2.5 Å from the anomeric carbon of α-GlcF, thereby explaining its apparent preference for production of ß-1,4-linked oligosaccharides. This functional and structural characterization provides the background for development of GH116 glycosynthases for synthesis of oligosaccharides and glycosides of interest.

Physiological Role of the Previously Unexplained Benzenetriol Dioxygenase Homolog in the Burkholderia sp. Strain SJ98 4-Nitrophenol Catabolism Pathway.

4-Nitrophenol, a priority pollutant, is degraded by Gram-positive and Gram-negative bacteria via 1,2,4-benzenetriol (BT) and hydroquinone (HQ), respectively. All enzymes involved in the two pathways have been functionally identified. So far, all Gram-negative 4-nitrophenol utilizers are from the genera Pseudomonas and Burkholderia. But it remains a mystery why pnpG, an apparently superfluous BT 1,2-dioxygenase-encoding gene, always coexists in the catabolic cluster (pnpABCDEF) encoding 4-nitrophenol degradation via HQ. Here, the physiological role of pnpG in Burkholderia sp. strain SJ98 was investigated. Deletion and complementation experiments established that pnpG is essential for strain SJ98 growing on 4-nitrocatechol rather than 4-nitrophenol. During 4-nitrophenol degradation by strain SJ98 and its two variants (pnpG deletion and complementation strains), 1,4-benzoquinone and HQ were detected, but neither 4-nitrocatechol nor BT was observed. When the above-mentioned three strains (the wild type and complementation strains with 2,2'-dipyridyl) were incubated with 4-nitrocatechol, BT was the only intermediate detected. The results established the physiological role of pnpG that encodes BT degradation in vivo. Biotransformation analyses showed that the pnpA-deleted strain was unable to degrade both 4-nitrophenol and 4-nitrocatechol. Thus, the previously characterized 4-nitrophenol monooxygenase PnpASJ98 is also essential for the conversion of 4-nitrocatechol to BT. Among 775 available complete genomes for Pseudomonas and Burkholderia, as many as 89 genomes were found to contain the putative pnpBCDEFG genes. The paucity of pnpA (3 in 775 genomes) implies that the extension of BT and HQ pathways enabling the degradation of 4-nitrophenol and 4-nitrocatechol is rarer, more recent, and likely due to the release of xenobiotic nitroaromatic compounds. IMPORTANCE An apparently superfluous gene (pnpG) encoding BT 1,2-dioxygenase is always found in the catabolic clusters involved in 4-nitrophenol degradation via HQ by Gram-negative bacteria. Our experiments reveal that pnpG is not essential for 4-nitrophenol degradation in Burkholderia sp. strain SJ98 but instead enables its degradation of 4-nitrocatechol via BT. The presence of pnpG genes broadens the range of growth substrates to include 4-nitrocatechol or BT, intermediates from the microbial degradation of many aromatic compounds in natural ecosystems. In addition, the existence of pnpCDEFG in 11.6% of the above-mentioned two genera suggests that the ability to degrade BT and HQ simultaneously is ancient. The extension of BT and HQ pathways including 4-nitrophenol degradation seems to be an adaptive evolution for responding to synthetic nitroaromatic compounds entering the environment since the industrial revolution.

Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-XL and BCL-2.

The BCL-2 family of proteins (including the prosurvival proteins BCL-2, BCL-XL, and MCL-1) is an important target for the development of novel anticancer therapeutics. Despite the challenges of targeting protein-protein interaction (PPI) interfaces with small molecules, a number of inhibitors (called BH3 mimetics) have entered the clinic and the BCL-2 inhibitor, ABT-199/venetoclax, is already proving transformative. For BCL-XL, new validated chemical series are desirable. Here, we outline the crystallography-guided development of a structurally distinct series of BCL-XL/BCL-2 inhibitors based on a benzoylurea scaffold, originally proposed as α-helix mimetics. We describe structure-guided exploration of a cryptic "p5" pocket identified in BCL-XL. This work yields novel inhibitors with submicromolar binding, with marked selectivity toward BCL-XL. Extension into the hydrophobic p2 pocket yielded the most potent inhibitor in the series, binding strongly to BCL-XL and BCL-2 (nanomolar-range half-maximal inhibitory concentration (IC50)) and displaying mechanism-based killing in cells engineered to depend on BCL-XL for survival.

A colorimetric microfluidic paper-based analytical device for sulfonamides in cow milk using enzymatic inhibition.

To increase milk production, antibiotics are administered to animals to provide weight gain and to prevent or treat diseases. The inappropriate use of these substances can lead to antibiotic resistance and allergic reactions and toxic effects to milk consumers. We describe the development of a simple, fast, portable, and low-cost microfluidic paper-based analytical device (µPAD) to quantify sulfonamides in milk using the inhibition of the colorimetric reaction between carbonic anhydrase (CA) and 4-nitrophenyl acetate. The main advantages presented by the µPAD include reproducible batch production, simple application, and precise analysis without previous treatment. The µPAD displayed good linearity (R2 ≥ 0.986) in a wide range of sulfonamides in milk (2.5 to 40.0 µmol L-1), being selective for the drugs even in a highly complex matrix. We expect that this device allows in situ monitoring of milk quality, reducing the prejudicial conditions associated with high concentrations of sulfonamides in milk.

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations.

We have performed multicanonical molecular dynamics (McMD) based dynamic docking simulations to study and compare the binding mechanism between two medium-sized inhibitors (ABT-737 and WEHI-539) that bind to the cryptic site of Bcl-xL, by exhaustively sampling the conformational and configurational space. Cryptic sites are binding pockets that are transiently formed in the apo state or are induced upon ligand binding. Bcl-xL, a pro-survival protein involved in cancer progression, is known to have a cryptic site, whereby the shape of the pocket depends on which ligand is bound to it. Starting from the apo-structure, we have performed two independent McMD-based dynamic docking simulations for each ligand, and were able to obtain near-native complex structures in both cases. In addition, we have also studied their interactions along their respective binding pathways by using path sampling simulations, which showed that the ligands form stable binding configurations via predominantly hydrophobic interactions. Although the protein started from the apo state, both ligands modulated the pocket in different ways, shifting the conformational preference of the sub-pockets of Bcl-xL. We demonstrate that McMD-based dynamic docking is a powerful tool that can be effectively used to study binding mechanisms involving a cryptic site, where ligand binding requires a large conformational change in the protein to occur.

Carboxylesterase Activities and Protein Expression in Rabbit and Pig Ocular Tissues.

Hydrolytic reactions constitute an important pathway of drug metabolism and a significant route of prodrug activation. Many ophthalmic drugs and prodrugs contain ester groups that greatly enhance their permeation across several hydrophobic barriers in the eye before the drugs are either metabolized or released, respectively, via hydrolysis. Thus, the development of ophthalmic drug therapy requires the thorough profiling of substrate specificities, activities, and expression levels of ocular esterases. However, such information is scant in the literature, especially for preclinical species often used in ophthalmology such as rabbits and pigs. Therefore, our aim was to generate systematic information on the activity and expression of carboxylesterases (CESs) and arylacetamide deacetylase (AADAC) in seven ocular tissue homogenates from these two species. The hydrolytic activities were measured using a generic esterase substrate (4-nitrophenyl acetate) and, in the absence of validated substrates for rabbit and pig enzymes, with selective substrates established for human CES1, CES2, and AADAC (d-luciferin methyl ester, fluorescein diacetate, procaine, and phenacetin). Kinetics and inhibition studies were conducted using these substrates and, again due to a lack of validated rabbit and pig CES inhibitors, with known inhibitors for the human enzymes. Protein expression levels were measured using quantitative targeted proteomics. Rabbit ocular tissues showed significant variability in the expression of CES1 (higher in cornea, lower in conjunctiva) and CES2 (higher in conjunctiva, lower in cornea) and a poor correlation of CES expression with hydrolytic activities. In contrast, pig tissues appear to express only CES1, and CES3 and AADAC seem to be either low or absent, respectively, in both species. The current study revealed remarkable species and tissue differences in ocular hydrolytic enzymes that can be taken into account in the design of esterase-dependent prodrugs and drug conjugates, the evaluation of ocular effects of systemic drugs, and in translational and toxicity studies.