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Microplastics (MPs) and nanoplastics (NPs) dispersed in agricultural ecosystems can pose a severe threat to biota in soil and nearby waterways. In addition, chemicals such as pesticides adsorbed by NPs can harm soil organisms and potentially enter the food chain. In this context, agriculturally utilized plastics such as plastic mulch films contribute significantly to plastic pollution in agricultural ecosystems. However, most fundamental studies of fate and ecotoxicity employ idealized and poorly representative MP materials, such as polystyrene microspheres. Therefore, as described herein, we developed a lab-scale multi-step procedure to mechanically form representative MPs and NPs for such studies. The plastic material was prepared from commercially available plastic mulch films of polybutyrate adipate-co-terephthalate (PBAT) that were embrittled through either cryogenic treatment (CRYO) or environmental weathering (W), and from untreated PBAT pellets. The plastic materials were then treated by mechanical milling to form MPs with a size of 46-840 µm, mimicking the abrasion of plastic fragments by wind and mechanical machinery. The MPs were then sieved into several size fractions to enable further analysis. Finally, the 106 µm sieve fraction was subjected to wet grinding to generate NPs of 20-900 nm, a process that mimics the slow size reduction process for terrestrial MPs. The dimensions and the shape for MPs were determined through image analysis of stereomicrographs, and dynamic light scattering (DLS) was employed to assess particle size for NPs. MPs and NPs formed through this process possessed irregular shapes, which is in line with the geometric properties of MPs recovered from agricultural fields. Overall, this size reduction method proved efficient for forming MPs and NPs composed of biodegradable plastics such as polybutylene adipate-co-terephthalate (PBAT), representing mulch materials used for agricultural specialty crop production.

Microplastics (MPs) have been widely distributed on Earth and have drawn global concern for freshwater and marine ecosystems. Biodegradable plastics have risen in popularity to replace nonbiodegradable plastics all over the world. The effects of biodegradable plastics on denitrifying and anammox bacteria in freshwater sediment remain largely unknown. In this study, water column reactors containing polylactic acid (PLA) or polybutylene adipate-co-terephthalate (PBAT) MPs in sediment were established to simulate lake ecosystems and analyze the effects of biodegradable MPs on sedimentary nitrogen transformation microorganisms. The total organic carbon (TOC) concentrations in the PLA and PBAT groups were slightly higher than those in the control group, which might be related to the slow degradation of these two plastics. Denitrifying and anammox bacterial diversities decreased after adding MPs to sediments for 30 days, and the dominant OTUs of these two bacteria were differentiated from the control. The abundance levels of nirS denitrifying and anammox bacteria on the PLA MP surface were significantly higher than those in the other groups (P 0.05), but they were lower in the PBAT groups than in the other groups. As an excellent electron donor for the denitrification process, lactic acid release from PLA degradation resulted in the enrichment of denitrifying and anammox bacteria on the MP surfaces. However, PBAT led to various responses of bacteria in an anaerobic environment. In addition, the redundancy analysis results indicated that total phosphorus, TOC and nitrate were strongly negatively correlated with the abundance levels of denitrifying and anammox bacteria. Our findings provided insight into the effects of MPs, especially the biodegradable ones, on sedimentary nitrogen-transformation bacteria.

Biodegradable plastic mulch film (BDM) is an environmentally friendly alternative to conventional polyethylene mulch, and has been growingly used in agriculture. However, practical degradation performance of BDM, especially the widely used type of blended polylactic acid (PLA)/polybutylene adipate (PBAT) in different ratios, and microbial alteration in soil environments, remain largely unrevealed. In this study, four types of BDM blended with 40-80% PLA and 20-60% PBAT were comparatively investigated through microcosm soil incubation experiments for 105 days, and combined with conditions of different soil moisture or pH. Microbiome within film-surrounding soil were assayed using 16 S rRNA high-throughput sequencing. Results showed a trend of increasing degradation efficiency with the increase of PLA proportion, and 70% PLA and 30% PBAT group presented the highest weight loss rate, i.e., 60.16 ± 5.86%. In addition, degradation and aging of PLA/PBAT varied among different soil moisture and pH values. A moderate moisture, i.e., 60% and a neutral pH7.0 caused significantly high degradation efficiency compared to other moisture or pH conditions. Moreover, bacterial abundance and community structure in the surrounding soil were related to soil moisture and pH. PLA/PBAT incubation treatment induced a remarkable increase in abundance of degradation-related species Pseudomonas and Sphingomonas. Bacterial richness and diversity in soil correspondingly respond to ratio-different PLA/PBAT's degradation under moisture/pH-different conditions through a redundancy analysis. Altogether, these findings indicate that practical degradation of PLA/PBAT film is closely related to soil environments and bacterial community. It is significant for the application of biodegradable plastics in agriculture on the perspective of soil sustainability.

Background Adipic acid (AA) is one of the most important industrial chemicals used mainly for the production of Nylon 6,6 but also for making polyurethanes, plasticizers, and unsaturated polyester resins, and more recently as a component in the biodegradable polyester poly(butylene adipate terephthalate) (PBAT). The main route for AA production utilizes benzene as feedstock and generates copious amounts of the greenhouse gas NO2. Hence, alternative clean production routes for AA from renewable bio-based feedstock are drawing increasing attention. We have earlier reported the potential of Gluconobacter oxydans cells to oxidize 1,6-hexanediol, a potentially biobased diol to AA. Results The present report involves a study on the effect of different parameters on the microbial transformation of 1,6-hexanediol to adipic acid, and subsequently testing the process on a larger lab scale for achieving maximal conversion and yield. Comparison of three wild-type strains of G. oxydans DSM50049, DSM2003, and DSM2343 for the whole-cell biotransformation of 10 g/L 1,6-hexanediol to adipic acid in batch mode at pH 7 and 30 °C led to the selection of G. oxydans DSM50049, which showed 100% conversion of the substrate with over 99% yield of adipic acid in 30 h. An increase in the concentrations of the substrate decreased the degree of conversion, while the product up to 25 g/L in batch and 40 g/L in fed-batch showed no inhibition on the conversion. Moreover, controlling the pH of the reaction at 5–5.5 was required for the cascade oxidation reactions to work. Cell recycling for the biotransformation resulted in a significant decrease in activity during the third cycle. Meanwhile, the fed-batch mode of transformation by intermittent addition of 1,6-hexanediol (30 g in total) in 1 L scale resulted in complete conversion with over 99% yield of adipic acid (approximately 37 g/L). The product was recovered in a pure form using downstream steps without the use of any solvent. Conclusion A facile, efficient microbial process for oxidation of 1,6-hexanediol to adipic acid, having potential for scale up was demonstrated. The entire process is performed in aqueous medium at ambient temperatures with minimal greenhouse gas emissions. The enzymes involved in catalyzing the oxidation steps are currently being identified.

Autism is a kind of biologically based neurodevelopmental condition, and the coexistence of atopic dermatitis (AD) is not uncommon. Given that the gut microbiota plays an important role in the development of both diseases, we aimed to explore the differences of gut microbiota and their correlations with urinary organic acids between autistic children with and without AD. We enrolled 61 autistic children including 36 with AD and 25 without AD. The gut microbiota was sequenced by metagenomic shotgun sequencing, and the diversity, compositions, and functional pathways were analyzed further. Urinary organic acids were assayed by gas chromatography–mass spectrometry, and univariate/multivariate analyses were applied. Spearman correlation analysis was conducted to explore their relationships. In our study, AD individuals had more prominent gastrointestinal disorders. The alpha diversity of the gut microbiota was lower in the AD group. LEfSe analysis showed a higher abundance of Anaerostipes caccae, Eubacterium hallii, and Bifidobacterium bifidum in AD individuals, with Akkermansia muciniphila, Roseburia intestinalis, Haemophilus parainfluenzae, and Rothia mucilaginosa in controls. Meanwhile, functional profiles showed that the pathway of lipid metabolism had a higher proportion in the AD group, and the pathway of xenobiotics biodegradation was abundant in controls. Among urinary organic acids, adipic acid, 3-hydroxyglutaric acid, tartaric acid, homovanillic acid, 2-hydroxyphenylacetic acid, aconitic acid, and 2-hydroxyhippuric acid were richer in the AD group. However, only adipic acid remained significant in the multivariate analysis (OR = 1.513, 95% CI [1.042, 2.198], P = 0.030). In the correlation analysis, Roseburia intestinalis had a negative correlation with aconitic acid (r = -0.14, P = 0.02), and the latter was positively correlated with adipic acid (r = 0.41, P = 0.006). Besides, the pathway of xenobiotics biodegradation seems to inversely correlate with adipic acid (r = -0.42, P = 0.18). The gut microbiota plays an important role in the development of AD in autistic children, and more well-designed studies are warranted to explore the underlying mechanism.

In order to synchronously improve mechanical and flame retardant properties of polylactide/poly(butylene adipate-co-terephthalate) (PLA/PBAT) composites, a series of multifunctional composites containing multi-walled carbon nanotubes (CNTs), ammonium polyphosphate (APP) and a commercial multifunctional epoxy oligomer (MEO) as chain extender were prepared via melt blending. The results show that the optimal flame retardant properties of PLA5-PBAT5/10A/6C composite containing 6 % CNTs and 10 wt% APP, presented the limited oxygen index reached 28.3 % and exhibited a decrease in peak heat release rate (pHRR) and total heat release (THR) to 368 kJ/m

In recent years, Poly(butylene adipate-co-terephthalate) (PBAT) films were wildly used due to its biodegradable properties. However, there are few reports of strains that can high efficiently degrade PBAT. Thermobifida fusca FXJ-1, a thermophilic actinomycete, was screened and identified from compost. FXJ-1 can efficiently degrade PBAT at 55 °C in MSM medium. The degradation rates of the pure PBAT film (PF), PBAT film used for mulching on agricultural fields (PAF), and PBAT-PLA-ST film (PPSF) were 82.87 ± 1.01%, 87.83 ± 2.00% and 52.53 ± 0.54%, respectively, after nine days of incubation in MSM medium. Cracking areas were monitored uniformly distributed on the surfaces of three kinds of PBAT-based films after treatment with FXJ-1 using scanning electron microscopy. The LC-MS results showed that PBAT might be degraded into adipic acid, terephthalic acid, butylene adipate, butylene terephthalate and butylene adipate-co-terephthalate, and these products are involved in the cleavage of ester bonds. We also found that amylase produced by FXJ-1 played an important role in the degradation of PPSF. FXJ-1 also showed an efficient PBAT-based films degradation ability in simulating compost environment, which implied its potential application in PBAT and starch-based film degradation by industrial composting.

Soil that contained polybutylene adipate-co-terephthalate (PBAT) was incubated with Priestia megaterium, Pseudomonas mendocina, and Pseudomonas pseudoalcaligenes to improve the biodegradative process of this polymer. The mixture of Pr. megaterium and Ps. mendocina was highly effective at biodegrading the PBAT, and after eight weeks of soil incubation, approximately 84% of the PBAT film weight was lost. Mixtures of the other two species also positively affected the synergistic degradation of PBAT film in the soil, but the mixture of three species had a negative effect. The residual PBAT film microstructure clearly demonstrated the degradation of PBAT, and the degree of degradation was related to the different species. Cleavage of the PBAT film ester bond after soil microbial action affected its properties. The incubation of PBAT in soil that contained these species affected soil dehydrogenase and soil lipase in particular. The secretion of lipase by these species could play an important role in the degradation of PBAT in the soil.

Xenobiotic chemical emissions from the informal electronic waste recycling (EW) sector are emerging problem for developing countries, with scale and impacts that are yet to be evaluated. We report an intensive polyurethane foam disk passive air sampling study in four megacities in India to investigate atmospheric organic pollutants along five transects viz., EW, information technology (IT), industrial, residential, and dumpsites. Intraurban emission sources were estimated and attributed by trajectory modeling and positive matrix factorization (PMF). ∑(17)PCDD/Fs, ∑(25)PCBs, ∑(7)plasticizers, and ∑(15)PAHs concentrations ranged from 3.1 to 26 pg/m(3) (14 ± 7; Avg ± SD), 0.5–52 ng/m(3) (9 ± 12); 7.5–520 ng/m(3), (63 ± 107) and 6–33 ng/m(3) (17 ± 6), respectively. EW contributed 45% of total PCB concentrations in this study and was evidenced as a major factor by PMF. The dominance of dioxin-like PCBs (dl-PCBs), particularly PCB-126, reflects combustion as the possible primary emission source. PCDD/Fs, PCBs and plasticizers were consistently highest at EW transect, while PAHs were maximum in industrial transect followed by EW. Concentrations of marker plasticizers (DnBP and DEHP) released during EW activities were significantly higher (p < 0.05) in Bangalore than in other cities. Toxic equivalents (TEQs) due to dl-PCBs was maximum in the EW transect and PCB-126 was the major contributor. For both youth and adult, the highest estimated inhalation risks for dl-PCBs and plasticizers were seen at the EW transect in Bangalore, followed by Chennai and New Delhi.

Accurate calculation of protein-protein binding free energy is of great importance in biological and medical science, yet it remains a hugely challenging problem. In this work, we develop a new strategy in which a screened electrostatic energy (i.e., adding an exponential damping factor to the Coulombic interaction energy) is used within the framework of the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Our results show that the Pearson correlation coefficient in the modified MM/PBSA is over 0.70, which is much better than that in the standard MM/PBSA, especially in the Amber14SB force field. In particular, the performance of the standard MM/PBSA is very poor in a system where the proteins carry like charges. Moreover, we also calculated the mean absolute error (MAE) between the calculated and experimental ΔG values and found that the MAE in the modified MM/PBSA was indeed much smaller than that in the standard MM/PBSA. Furthermore, the effect of the dielectric constant of the proteins and the salt conditions on the results was also investigated. The present study highlights the potential power of the modified MM/PBSA for accurately predicting the binding energy in highly charged biosystems.

In recent years, poly (butylene adipate-co-terephthalate) (PBAT) has been widely used. However, PBAT-degrading bacteria have rarely been reported. PBAT-degrading bacteria were isolated from farmland soil and identified. The effects of growth factors on the degradation of PBAT and the lipase activity of PBAT-degrading bacteria were assessed. The degradation mechanism was analyzed using scanning electron microscopy, attenuated total reflection Fourier transform infrared spectroscopy, proton nuclear magnetic resonance, X-ray diffraction, and liquid chromatography-mass spectrometry. The results showed that Stenotrophomonas sp. YCJ1 had a significant degrading effect on PBAT. Under certain conditions, the strain could secrete 10.53 U/mL of lipase activity and degrade 10.14 wt.% of PBAT films. The strain secreted lipase to catalyze the degradation of the ester bonds in PBAT, resulting in the production of degradation products such as terephthalic acid, 1,4-butanediol, and adipic acid. Furthermore, the degradation products could participate in the metabolism of YCJ1 as carbon sources to facilitate complete degradation of PBAT, indicating that the strain has potential value for the bioremediation of PBAT in the environment.

The dicarbonylation of 1,3‐butadiene to adipic acid derivatives offers the potential for a more cost‐efficient and environmentally benign industrial process. However, the complex reaction network of regioisomeric carbonylation and isomerization pathways, make a selective and direct transformation particularly difficult. Here, we report surprising solvent effects on this palladium‐catalysed process in the presence of 1,2‐bis‐di‐tert‐butylphosphin‐oxylene (dtbpx) ligands, which allow adipate diester formation from 1,3‐butadiene, carbon monoxide, and methanol with 97 % selectivity and 100 % atom‐economy under scalable conditions. Under optimal conditions a variety of di‐ and triesters from 1,2‐ and 1,3‐dienes can be obtained in good to excellent yields., High value‐added conversion: From gas to nylon precursor. This 100 % atom economic and industrially relevant process is strongly influenced by the system polarity.

Biodegradation tests of chitosan (CH), polybutylene adipate terephthalate (PBAT) and high density polyethylene (HDPE) polymers were carried out using the standard OECD 301D guidelines. The results showed that the CH samples biodegraded faster than those of PBAT. Photographs registered exhibited the complete or partial disintegration of the samples, and a more opaque color was observed with the increase of biodegradation. FTIR analysis showed some changes in the intensity of the typical bands of the HDPE sample. The presence of P. nitroreducens bacteria was revealed on the PBAT sample surface by SEM studies. Additionally, a clear increase in elastic modulus (EM) and tensile strength (TS) values were observed in PBAT and HDPE samples on day 3, which decreased significantly at the end of the study. Furthermore, an increase in the crystallinity of the HDPE sample was observed on day 28.

Thermosetting polymeric materials have advantageous properties and are therefore used in numerous applications. In this study, it was hypothesized and ultimately shown that thermosets could be derived from comparably sustainable sub-components. A two-step procedure to produce a thermoset comprising of Kraft lignin (KL) and the cross-linker adipic acid (AdA) was developed. The cross-linking was activated by means of an acetylating agent comprising isopropenyl acetate (IPA) to form a cross-linking mixture (CLM). The cross-linking was confirmed by FTIR and solid-state NMR spectroscopy, and the esterification reactions were further studied using model compounds. When the KL lignin was mixed with the CLM, partial esterification occurred to yield a homogeneous viscous liquid that could easily be poured into a mold, as the first step in the procedure. Without any additions, the mold was heated and the material transformed into a thermoset by reaction of the two carboxylic acid-derivatives of AdA and KL in the second step.

The degradable plastic poly(butylene adipate-co-terephthalate) (PBAT) is considered a potential replacement for low-density polyethylene (LDPE) as the main component of mulch film. However, it is not clear whether PBAT is harmful to the plant-soil system. Thus, we determined the effects of LDPE microplastics (LDPE-MPs) and PBAT microplastics (PBAT-MPs) on the growth of Arabidopsis. The inhibitory effect of PBAT-MPs was greater than that of LDPE-MPs on the growth of Arabidopsis. Transcriptome analysis showed that PBAT-MPs severely disrupted the photosynthetic system of Arabidopsis and increased the expression levels of genes in drug transport-related pathways. PBAT-MPs increased the relative abundances of Bradyrhizobium, Hydrogenophaga, and Arthrobacter in the bulk soil and rhizosphere soil. The abundances of Variovorax, Flavobacterium, and Microbacterium increased in the plant root zone only under PBAT-MPs. Functional prediction analysis suggested that microorganisms in the soil and plant root zone could degrade xenobiotics. Furthermore, the degradation products from PBAT comprising adipic acid, terephthalic acid, and butanediol were more toxic than PBAT-MPs. Our findings demonstrate that PBAT-MPs may be degraded by microorganisms to produce chemicals that are highly toxic to plants. Thus, biodegradable plastics may pose a great risk to the environment.

Pimelic acid is an important seven-carbon dicarboxylic acid, which is broadly applied in various fields. The industrial production of pimelic acid is mainly through a chemical method, which is complicated and environmentally unfriendly. Herein, we found that pimelic acid could be biosynthesized by the reverse adipate-degradation pathway (RADP), a typical Claisen condensation reaction that could be applied to the arrangement of C-C bond. In order to strengthen the supply of glutaryl-CoA precursor, PA5530 protein was used to transport glutaric acid. Subsequently, we discovered that the enzymes in the BIOZ pathway are isoenzyme of the RADP pathway enzymes. By combining the isoenzymes of the two pathways, the titer of pimelic acid reached 36.7 mg ⋅ L

Efficient catalytic ring-opening coupled with hydrogenation is a promising but challenging reaction for producing adipic acid (AA) from 2,5-furan dicarboxylic acid (FDCA). In this study, AA synthesis is carried out in two steps from FDCA via tetrahydrofuran-2,5-dicarboxylic acid (THFDCA) over a recyclable Ru/Al

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the contagious coronavirus disease 2019 (COVID-19) which was first identified in Wuhan, China, in December 2019. Around the world, many researchers focused their research on identifying inhibitors against the druggable SARS-CoV-2 targets. The reported genomic mutations have a direct effect on the receptor-binding domain (RBD), which interacts with host angiotensin-converting enzyme 2 (ACE-2) for viral cell entry. These mutations, some of which are variants of concern (VOC), lead to increased morbidity and mortality rates. The newest variants including B.1.617.2 (Delta), AY.1 (Delta plus), and C.37 (Lambda) were considered in this study. Thus, an exhaustive structure-based virtual screening of a ligand library (in which FDA approved drugs are also present) using the drug-likeness screening, molecular docking, ADMET profiling was performed followed by molecular dynamics (MD) simulation, and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculation to identify compounds or drugs can be repurposed for inhibiting the wild type, Delta, Delta plus and Lambda variants of RBD of the spike protein. Based on the virtual screening steps, two FDA approved drugs, Atovaquone (atv) and Praziquantel (prz), were selected and repurposed as the best candidates of SARS-CoV-2 RBD inhibitors. Molecular docking results display that both atv and prz contribute in different interaction with binding site residues (Gln493, Asn501 and Gly502 in the hydrogen bond formation, Phe490 and Tyr505 in the π- π stacking and Tyr449, Ser494, and Phe497 in the vdW interactions) in the wild type, Delta, Delta plus and Lambda variants of RBD of the spike protein. MD simulations revealed that among the eight studied complexes, the wild type-atv and Delta-prz complexes have the most structural stability over the simulation time. Furthermore, MM-PBSA calculation showed that in the atv containing complexes, highest binding affinity is related to the wild type-atv complex and in the prz containing complexes, it is related to the Delta-prz complex. The validation of docking results was done by comparing with experimental data (heparin in complex with wild type and Delta variants). Also, comparison of the obtained results with the result of simulation of the k22 with the studied proteins showed that atv and prz are suitable inhibitors for these proteins, especially wild type t and Delta variant, respectively. Thus, we found that atv and prz are the best candidate for inhibition of wild type and Delta variant of the spike protein. Also, atv can be an appropriate inhibitor for the Lambda variant. Obtained in silico results may help the development of new anti-COVID-19 drugs.

Pimelic acid, a seven carbon α,ω-dicarboxylic acid (heptanedioic acid), is known to provide seven of the ten biotin carbon atoms including all those of the valeryl side chain. Distinct pimelate synthesis pathways were recently elucidated in Escherichia coli and Bacillus subtilis where fatty acid synthesis plus dedicated biotin enzymes produce the pimelate moiety. In contrast, the α-proteobacteria which include important plant and mammalian pathogens plus plant symbionts, lack all of the known pimelate synthesis genes and instead encode bioZ genes. Here we report a pathway in which BioZ proteins catalyze a 3-ketoacyl-acyl carrier protein (ACP) synthase III-like reaction to produce pimeloyl-ACP with five of the seven pimelate carbon atoms being derived from glutaryl-CoA, an intermediate in lysine degradation. Agrobacterium tumefaciens strains either deleted for bioZ or which encode a BioZ active site mutant are biotin auxotrophs, as are strains defective in CaiB which catalyzes glutaryl-CoA synthesis from glutarate and succinyl-CoA., Biosynthesis of biotin precursor, pimelate moiety, is elucidated in Escherichia coli and Bacillus subtilis, but not understood in alphaproteobacteria. Here, the authors show that BioZ, a 3-ketoacyl-ACP synthase, catalayses pimeloyl-thioester synthesis in alphaproteobacteria using malonyl-ACP and glutaryl-CoA that is derived from lysine degradation.

Adipic Acid (AA) is a valued platform chemical compound, which can be used as a precursor of nylon-6,6. Due to the generation of an enormous amount of nitric oxide metabolites and the growing depletion of oil resources as a result of AA production from a mixture of cyclohexanol and cyclohexanone, the microbial methods for synthesizing AA have attracted significant attention. Of the several AA-producing pathways, the reverse adipate degradation pathway in Thermobifida fusca (Tfu RADP) is reported to be the most efficient, which has been confirmed in Escherichia coli. In this study, the heterologous Tfu RADP was constructed for producing AA in S. cerevisiae by co-expressing genes of Tfu_0875, Tfu_2399, Tfu_0067, Tfu_1647, Tfu_2576, and Tfu_2576. The AA titer combined with biomass, cofactors and other by-products was all determined after fermentation. During batch fermentation in a shake flask, the maximum AA titer was 3.83 mg/L, while the titer increased to 10.09 mg/L during fed-batch fermentation in a 5-L bioreactor after fermentation modification.

The SARS-cov-2 RNA dependent RNA polymerase (nsp12) is a crucial viral enzyme that catalyzes the replication of RNA from RNA templates. The fixation of some ligands in the active site may alter the viral life cycle. The aim of the present study is to identify the conservation level of nsp12 motifs (A-G), using consurf server, and discover their interactions with rifabutin, rifampicin, rifapentin, sorangicin A, streptolydigin, myxopyronin B, VXR and VRX using AutoDockTools-1.5.6, Gromacs 2018.2 and g-mmpbsa. Thus, the most of amino acids residues located in nsp12 protein Motifs (A-G) were predicted as highly conserved. The binding energies of streptolydigin, VXR, rifabutin, rifapentine, VRX, sorangicin A, myxopyronin B and rifampicin with nsp12 protein are -8.11, -8.23, -7.14, -6.94, -6.55, -5.46, -5.33 and -5.26 kcal/mol, respectively. In the other hand, the binding energies of ligand in the same order with nsp7-nsp8-nsp12 complex are -7.23, -7.08, -7.21, -7, -6.59, -8.73, -5.52, -5.87 kcal/mol, respectively. All ligands interact with at least two nsp12 motifs. The molecular dynamics simulation of nsp12-streptolydigin and nsp12-VXR complexes shows that these two complexes are stable and the number of hydrogen bonds as a function of time, after 30 ns of simulation, varies between 0 and 6 for nsp12-streptolydigin complex and between 0 and 4 for nsp12-VXR complex. The average of free binding energies obtained using g_mmpbsa, after 30 ns of simulation, is -191.982 Kj/mol for nsp12-streptolydigin complex and -153.583 Kj/mol for nsp12-VXR complex. Our results suggest that these ligands may be used as inhibitors of SARS-cov-2 nsp12 protein. Communicated by Ramaswamy H. Sarma.

Binding of calcium ion to calcium-binding proteins (CBP) triggers a large number of biological processes in a cell. CBP are known to play important roles in various diseases, such as cancer, alzheimer, and neuronal problems. However, the calculation of the binding affinity of calcium ion to CBP still possesses a significant challenge to the computational investigators. One of the main reasons for this difficulty is the polarization of CBP due to the binding of calcium. In the current work, we have used the implicit polarization method of Leontyev et al. (PCCP, 13.7 (2011): 2613-2626) to calculate the binding free energy of calcium ion binding to calmodulin, an important CBP. We have used the widely used MM-PBSA method to find a good protocol of calculation with implicit polarization. We have also optimized the best value of the calcium radius to match the experimental results. Our results show incorporation of polarization improves the agreement between the calculated and experimental results, although still, some discrepancy remains. On the whole, this work shows implicit polarization when combined with the MM-PBSA method can give results better than calculation without any polarization, and further improvement is necessary to get a quantitative match with experiments. Communicated by Ramaswamy H. Sarma

Background Although more information has become available on the occurrence of phthalates and di(2-ethylhexyl) adipate (DEHA) in foods including cow’s milk, information on their presence in human milk, the important and recommended sole diet for infants up to six months of age, is very limited, especially for DEHA. Objective To develop a GC-MS method for simultaneous analysis of DEHA and phthalates in human milk samples and generate occurrence data for exposure assessment. Method Human milk samples were extracted with acetonitrile followed by dispersive solid-phase extraction and GC-MS analysis. Results Among the 305 human milk samples collected from the Canadian Maternal-Infant Research on Environmental Chemicals Study, some phthalates (DHxP, BBzP, and DOP) were not detected in any of the samples, while DEHA and the other phthalates (DMP, DEP, DBP, DiBP, and DEHP) were detected at low frequencies with levels from 30.4–237 ng/g in up to 31 of the 305 human milk samples. Conclusions In general, DEHA and phthalates were detected at low frequencies and low levels in the 305 human milk samples. Highlights A GC-MS method based on dispersive solid phase extraction was developed for analysis of DEHA and eight phthalates in 305 human milk samples for exposure assessment.

The synergistic effects of the combination of acetylated distarch adipate and sesbania gum (C-ADA-SG) with the ratio of 5:0, 4:1, 2.5:2.5, 1:4, 0:5, accounting for 5% (w/w) of the starch on gelatinization and retrogradation properties of wheat starch (WS) were studied. Scanning Electron Microscopy (SEM) showed that the microstructure of gelatinized WASs (WS added with C-ADA-SG) tended to be smoother. Based on the results of Rapid Visco-Analyzer (RVA) and Differential Scanning Calorimetry (DSC), the pasting characteristics of WS were affected and the gelatinization process was retarded by C-ADA-SG. After seven-day storage at 4 °C, compared to WS, the gel firmness, syneresis, retrogradation enthalpy, and the relative crystallinity of WASs clearly decreased by 17.47–44.36 g, 11.16–17.93%, 0.22–0.80 J·g−1, and 4.06–8.61%, respectively. However, the band ratio 1639:1157 cm−1 by FTIR and loss tangent (tan δ) value were increased with C-ADA-SG addition. Meanwhile, X-Ray Diffraction (XRD) reflected that native WS showed A-type crystal structure, which transferred to B + V type after retrogradation. Furthermore, Low-Field Nuclear Magnetic Resonance (LF-NMR) declared that C-ADA-SG increased the water mobility and limited the diffusion and seepage of water during storage. Generally, ADA and SG produced a synergistic effect on retarding the gelatinization and retrogradation of WS.

Background Prosthesis infection is a difficult-to-treat situation. Hydrogel is a novel biomaterial, which can be applied by simply spraying or by coating on implants before surgery and can be easily mixed with antibiotics. Methods In order to evaluate the potential use of antibiotic-loaded hydrogel, we incorporated vancomycin into oxidized hyaluronic acid (HA) and adipic acid dihydrazide and evaluated the drug release and antimicrobial activity against methicillin-resistant Staphylococcus aureus (ATCC 29213). Results The average release percentage of vancomycin on day 3 was about 86%. The antibiotic-loaded gel was biocompatible with mesenchymal stem cell, MC3T3, and L929 cell lines. The in vitro inhibition zones of vancomycin-loaded hydrogel [500X minimal inhibition concentration (MIC), 50X MIC, 10X MIC, and blank hydrogel] were 21, 13, 9, and 5 mm, respectively. In the Ti6Al4V implant biofilm model, 0.01–1% vancomycin-loaded gel exhibited significant anti-biofilm activity, measured by the MTT assay. Conclusions Vancomycin could be loaded onto oxidized HA and adipic acid dihydrazide, which exhibited excellent drug release and in vitro antimicrobial activity with minimal cell toxicity.

The widespread of the COVID-19 disease, caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), had severely affected the entire world. Unfortunately, no successful vaccines or antiviral drugs are currently available which leaves the scientific community under huge pressure to tackle this pandemic. Among the identified promising druggable targets, specific to this virus, is the main protease (Mpro) enzyme, which is vital for viral replication, transcription and packaging within the host cells. In this study, selective inhibition of the Mpro was sought via thorough analysis of its available structural data in the Protein Data Bank. To this end, COVID-19 Mpro crystal complexes were explored and the key interacting residues (KIRs) within its active site, that are expected to be vital for effective ligand binding, were identified. Based on these KIRs, 3D pharmacophore models were generated and used in virtual screening of different databases. Retrieved hits were docked into the active site of the enzyme and their MM-PBSA based free binding energies were calculated. Finally, ADMET descriptors were calculated to aid the selection of top scoring hits with best ADMET properties. Nine compounds with different chemotypes were identified as potential Mpro inhibitors. Further, MD simulations of a virtual complex of Mpro with one of the promising hits revealed stable binding which is indicative of good inhibitory potential. The identified compounds in this study are expected to support the global drug discovery efforts in fighting against this highly contagious virus by narrowing the searchable chemical space for potential effective therapeutics. Communicated by Ramaswamy H. Sarma

Rapid evolution of enzyme activities is often hindered by the lack of efficient and affordable methods to identify beneficial mutants. We report the development of a new growth-coupled selection method for evolving NADPH-consuming enzymes based on the recycling of this redox cofactor. The method relies on a genetically modified Escherichia coli strain, which overaccumulates NADPH. This method was applied to the engineering of a carboxylic acid reductase (CAR) for improved catalytic activities on 2-methoxybenzoate and adipate. Mutant enzymes with up to 17-fold improvement in catalytic efficiency were identified from single-site saturated mutagenesis libraries. Obtained mutants were successfully applied to whole-cell conversions of adipate into 1,6-hexanediol, a C6 monomer commonly used in polymer industry.

International audience; The goal of this study was to determine the potential exposure of much of the French population to nine phthalates and bis (2-ethylhexyl) adipate (DEHA) due to water consumption. The occurrence of these compounds was investigated in raw and treated water from public water systems. Water samples were collected in one sampling campaign equally distributed across 101 French départements (a French administrative unit) from November 2015 to July 2016. In all, 271 raw water samples and 283 treated water samples were collected. A specific sampling protocol was conducted in order to assess phthalate pollution during sampling and analysis, and to produce reliable results. Field blanks were thus collected at the same time as real samples at each sampling point. The contamination detected in field blanks was due to diethyl phthalate (DEP), dibutyl phthalate (DBP), diisobutyl phthalate (DIBP), and di-2-ethylhexyl phthalate (DEHP), which are common phthalate interferences in blanks. Their concentrations were never ten times higher than the limits of quantification (LOQ). In tap water, the most frequently detected compound was DBP, at a maximum concentration of 1300 ng/L. In raw water, however, DEP was the most frequently detected analyte with concentrations ranging from 255 to 406 ng/L, while DIBP was observed at a maximum concentration of 1650 ng/L. It is worth mentioning that DEHP-the most widely used phthalate-was only detected in one sample of raw water. Phthalates are not concentrated in any particular area of France in either raw or treated water.

Rheumatoid Arthritis (RA) is an autoimmune disease caused by overproduction of pro-inflammatory cytokines. Janus Kinases (JAKs) mediate cytokines signaling through the Janus Kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathways. Clinical studies have shown that Janus kinase 1 (JAK1) mediated signaling plays a key role in synovial response in rheumatoid arthritis. Hence, the inhibition JAK1 is considered as an important therapeutic route for treatment of rheumatoid arthritis. In this study, we have performed three-dimensional quantitative structure-activity relationship (3 D-QSAR), molecular docking, molecular dynamics (MD) and free energy calculations on a series of pyrrolo[2,3-d]pyrimidin-4-amine JAK1 inhibitors. Molecular docking studies of the compounds 03, 13, 36 and 49 with JAK1 were performed to study the binding interactions. The binding conformations of the compounds from docking studies were selected based on binding energy and H-bond interactions and were used as initial structure for MD simulations. Using 3 D-QSAR techniques, a ligand-based comparative molecular field analysis (CoMFA) model (q2 = 0.5, r2 = 0.96) and a receptor-based CoMFA model (q2 = 0.78, r2 = 0.98) were developed. Analysis of the MD results of the most active compound (compound 49) with JAK1 showed the formation of H-bond interactions with residues Glu957, Leu959 and Gly887 and water-mediated H-bond interaction with Gly887 and His885. Based on the contour map analyses of the receptor-based CoMFA, a design strategy was proposed and was used for designing new JAK1 inhibitors. Four of the designed compounds (D57, D58, D98 and D99) showed predicted activity values (pIC50> 8.8) greater than the most active compound for JAK1. MM-PBSA based free energy calculations indicated that the designed compounds were able to form stable binding with JAK1 primarily through electrostatic interactions and van der Waal interactions. Collectively, the outcome of this study can be used to further the progress of JAK1 inhibition for the treatment of rheumatoid arthritis. Communicated by Ramaswamy H. Sarma

Accurate calculation of the binding free energies between a protein and a ligand is the primary objective of structure-based drug design, but it still remains a challenging problem. In this work, we apply the screening molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) method to calculate the binding affinity of protein-ligand interactions. Our results show that the performance of the screening MM/PBSA is better than that of the standard MM/PBSA, especially in a charged-ligand system. In addition, we also investigate the effect of the solute dielectric constant on the results, and find that the optimal solute dielectric constants are different between the neutral-ligand system and the charged-ligand system. Moreover, we also evaluate the effect of the atomic-charge methods on the performance of the screening MM/PBSA. The present study demonstrates that the screening MM/PBSA should be a reliable method for calculating binding energy of biosystems.

Poly (butylene adipate-co-terephthalate) (PBAT)/polylactic acid (PLA) blended with compatibilizers (polycaprolactone, PCL; poly (ethylene glycol), PEG; titanium dioxide, nano-TiO

The BRPF1 protein is encoded by the BRPF1 gene. In addition, the BRPF1 gene is known to be upregulated in leukaemia. Recent studies have shown that it is also overexpressed in hepatocellular carcinoma (HCC) as well. Therefore, BRPF1 is a significant target for anti-cancer drug development studies, especially on HCC. 40 terpenoids and flavonoids were chosen because of their anticancer properties given in the literature. In this study, the biological activity of molecules was also investigated with in silico structure-activity relationship analysis. In addition, interactions between a series of terpenoids and flavonoids and the BRPF1 protein were investigated by molecular docking and molecular dynamics simulations. The energy change caused by the interactions of BRPF1 with different compounds was also evaluated by MM/PBSA calculations. It has been revealed that compound 5 (-9.2 kcal/mol), a kind of secoclerodane type diterpenoid, has a higher affinity both compared to other flavonoids and terpenoids, and 9F9 (-7.9 kcal/mol), a selective BRPF1 inhibitor. The study presented in this article demonstrates that compound 5, as a natural product, could form a chemical scaffold for the development of selective BRPF1 bromodomain inhibitors. European Cooperation in Science and Technology (COST) CA17104

In this paper we present a novel strategy to easily prepare biodegradable chitosan derived films as new packaging systems. Combination of chitosan, adipic acid and 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methyl-morpholinium chloride (DMTMM) allowed to obtain high-performing cross-linked films. Biobased glycerol was employed as plasticizer. An in-depth study was performed on ten different samples in order to evaluate the role of DMTMM as cross-linking agent. Experimental data showed that 15 wt% of DMTMM enhanced moisture content and moisture uptake (10.42% and 11.11%), water vapor permeability (0.13 10

In the present study, the ammonium formate version of the QuEChERS method, considered highly advantageous in relation to instrument maintenance and other issues, was applied for the first time to extract a group of twelve phthalic acid esters (PAEs, i.e. dipropyl phthalate, DPP; diisobutyl phthalate, DIBP; dibutyl phthalate, DBP; diisopentyl phthalate, DIPP; di-n-pentyl phthalate, DNPP; dihexyl phthalate, DHP; butyl benzyl phthalate, BBP; dicyclohexyl phthalate, DCHP; di(2-ethylhexyl) phthalate, DEHP; di-n-octyl phthalate, DNOP; diisononyl phthalate, DINP; and diisodecyl phthalate, DIDP) and one adipate (di(2-ethylhexyl) adipate, DEHA) from two species of fish (Scomber colias and Katsuwonus pelamis) and one of squid (Loligo gahi). The method was validated in terms of linearity, trueness and matrix effects. Determination coefficients (R

Production of platform chemicals from renewable feedstocks is becoming increasingly important due to concerns on environmental contamination, climate change, and depletion of fossil fuels. Adipic acid (AA), 6-aminocaproic acid (6-ACA) and 1,6-hexamethylenediamine (HMD) are key precursors for nylon synthesis, which are currently produced primarily from petroleum-based feedstocks. In recent years, the biosynthesis of adipic acid from renewable feedstocks has been demonstrated using both bacterial and yeast cells. Here we report the biocatalytic conversion/transformation of AA to 6-ACA and HMD by carboxylic acid reductases (CARs) and transaminases (TAs), which involves two rounds (cascades) of reduction/amination reactions (AA → 6-ACA → HMD). Using purified wild type CARs and TAs supplemented with cofactor regenerating systems for ATP, NADPH, and amine donor, we established a one-pot enzyme cascade catalyzing up to 95% conversion of AA to 6-ACA. To increase the cascade activity for the transformation of 6-ACA to HMD, we determined the crystal structure of the CAR substrate-binding domain in complex with AMP and succinate and engineered three mutant CARs with enhanced activity against 6-ACA. In combination with TAs, the CAR L342E protein showed 50-75% conversion of 6-ACA to HMD. For the transformation of AA to HMD (via 6-ACA), the wild type CAR was combined with the L342E variant and two different TAs resulting in up to 30% conversion to HMD and 70% to 6-ACA. Our results highlight the suitability of CARs and TAs for several rounds of reduction/amination reactions in one-pot cascade systems and their potential for the biobased synthesis of terminal amines.

A 2 : 1 urea ⋅ adipic acid cocrystal was obtained in two polymorphic forms (Form I reported earlier, and Form II synthesized in this study) using mechanochemistry as well as solution crystallization. Lower solubility and leaching study showed the newly synthesized urea ⋅ adipic acid 2 : 1 cocrystal to be an efficient sustained-release nitrogen fertilizer compared to commercially available urea.

In this work, the ammonium formate version of the QuEChERS method has been applied for the first time to the extraction of a group of nine phthalic acid esters and one adipate from three types of coffee (maximum intensity, intermediate intensity and decaffeinated) prepared from coffee capsules, using gas chromatography coupled to mass spectrometry for analytes separation and determination. Matrix-matched calibration showed good linearity with determination coefficients (R