β-Carboline alkaloids induce structural plasticity and inhibition of SARS-CoV-2 nsp3 macrodomain more potently than remdesivir metabolite GS-441524: computational approach

The nsp3 macrodomain is implicated in the viral replication, pathogenesis and host immune responses through the removal of ADP-ribosylation sites during infections of coronaviruses including the SARS-CoV-2. It has ever been modulated by macromolecules including the ADP-ribose until Ni and co-workers recently reported its inhibition and plasticity enhancement unprecedentedly by remdesivir metabolite, GS-441524, creating an opportunity for investigating other biodiverse small molecules such as β-Carboline (βC) alkaloids. In this study, 1497 βC analogues from the HiT2LEAD chemical database were screened, using computational approaches of Glide XP docking, molecular dynamics simulation and pk-CSM ADMET predictions. Selectively, βC ligands, 129, 584, 1303 and 1323 demonstrated higher binding affinities to the receptor, indicated by XP docking scores of –10.72, –10.01, –9.63 and –9.48 kcal/mol respectively than remdesivir and GS-441524 with –4.68 and –9.41 kcal/mol respectively. Consistently, their binding free energies were –36.07, –23.77, –24.07 and –17.76 kcal/mol respectively, while remdesivir and GS-441524 showed –21.22 and –24.20 kcal/mol respectively. Interestingly, the selected βC ligands displayed better stability and flexibility for enhancing the plasticity of the receptor than GS-441524, especially 129 and 1303. Their predicted ADMET parameters favour druggability and low expressions for toxicity. Thus, they are recommended as promising adjuvant/standalone anti-SARS-CoV-2 candidates for further study.Key words: SARS-CoV-2, nsp3 macrodomain, ADP-ribose, β-carboline, bioinformatics, drug design     

A peroxisomal thioesterase plays auxiliary roles in plant β‐oxidative benzoic acid metabolism

Peroxisomal β‐oxidative degradation of compounds is a common metabolic process in eukaryotes. Reported benzoyl‐coenzyme A (BA‐CoA) thioesterase activity in peroxisomes from petunia flowers suggests that, like mammals and fungi, plants contain auxiliary enzymes mediating β‐oxidation. Here we report the identification of Petunia hybrida thioesterase 1 (PhTE1), which catalyzes the hydrolysis of aromatic acyl‐CoAs to their corresponding acids in peroxisomes. PhTE1 expression is spatially, developmentally and temporally regulated and exhibits a similar pattern to known benzenoid metabolic genes. PhTE1 activity is inhibited by free coenzyme A (CoA), indicating that PhTE1 is regulated by the peroxisomal CoA pool. PhTE1 downregulation in petunia flowers led to accumulation of BA‐CoA with increased production of benzylbenzoate and phenylethylbenzoate, two compounds which rely on the presence of BA‐CoA precursor in the cytoplasm, suggesting that acyl‐CoAs can be exported from peroxisomes. Furthermore, PhTE1 downregulation resulted in increased pools of cytoplasmic phenylpropanoid pathway intermediates, volatile phenylpropenes, lignin and anthocyanins. These results indicate that PhTE1 influences (i) intraperoxisomal acyl‐CoA/CoA levels needed to carry out β‐oxidation, (ii) efflux of β‐oxidative products, acyl‐CoAs and free acids, from peroxisomes, and (iii) flux distribution within the benzenoid/phenylpropanoid metabolic network. Thus, this demonstrates that plant thioesterases play multiple auxiliary roles in peroxisomal β‐oxidative metabolism.     

Influence of lactic cultures on the quality attributes of tsire,a West African stick meat

Tsire is a popular, traditionally processed West African stick meat. Two lactic acid bacteria (LAB), Pediococcus acidi-lactici and Lactobacillus plantarum were used to inoculate pieces of fresh beef before (TA) and after (TB) grilling followed by incubation at 30 °C for 24 h. TA and TB tsire samples had the lowest coliform count (expressed as log c.f.u./g) of 13.48 and 8.83, Staphylococcus count of 7.90 and 5.76, Pseudomonas count of 10.06 and 5.99 on day 6 of storage period respectively. There was an increase in the population of the inoculated LAB in the TA and TB samples to 10.93 and 12.41 respectively. However, the uninoculated samples (TU) had a relatively high coliform, Staphylococcus and Pseudomonas counts. Biochemical analysis of the tsire products showed the TB samples having the highest crude protein (26.43%), thiobarbituric acid (0.25 mg malonaldehyde/kg) and free fatty acid (0.45 mg KOH/g lipid) values. Polyvinyl chloride was found to be the most suitable packaging material for the products during storage, compared with aluminium foil and newsprint. Organoleptic evaluation of the tsire samples also revealed that the TB samples were rated higher in terms of texture, appearance and flavour, while the uninoculated samples had the lowest scores.     

A Genome-Wide Investigation of MicroRNA Expression Identifies Biologically-Meaningful MicroRNAs That Distinguish between High-Risk and Low-Risk Intraductal Papillary Mucinous Neoplasms of the Pancreas

Background

Intraductal papillary mucinous neoplasms (IPMNs) are pancreatic ductal adenocarcinoma (PDAC) precursors. Differentiating between high-risk IPMNs that warrant surgical resection and low-risk IPMNs that can be monitored is a significant clinical problem, and we sought to discover a panel of mi(cro)RNAs that accurately classify IPMN risk status.

Methodology/Principal Findings

In a discovery phase, genome-wide miRNA expression profiling was performed on 28 surgically-resected, pathologically-confirmed IPMNs (19 high-risk, 9 low-risk) using Taqman MicroRNA Arrays. A validation phase was performed in 21 independent IPMNs (13 high-risk, 8 low-risk). We also explored associations between miRNA expression level and various clinical and pathological factors and examined genes and pathways regulated by the identified miRNAs by integrating data from bioinformatic analyses and microarray analysis of miRNA gene targets. Six miRNAs (miR-100, miR-99b, miR-99a, miR-342-3p, miR-126, miR-130a) were down-regulated in high-risk versus low-risk IPMNs and distinguished between groups (P<10⁻³, area underneath the curve (AUC) = 87%). The same trend was observed in the validation phase (AUC = 74%). Low miR-99b expression was associated with main pancreatic duct involvement (P = 0.021), and serum albumin levels were positively correlated with miR-99a (r = 0.52, P = 0.004) and miR-100 expression (r = 0.49, P = 0.008). Literature, validated miRNA:target gene interactions, and pathway enrichment analysis supported the candidate miRNAs as tumor suppressors and regulators of PDAC development. Microarray analysis revealed that oncogenic targets of miR-130a (ATG2B, MEOX2), miR-342-3p (DNMT1), and miR-126 (IRS-1) were up-regulated in high- versus low-risk IPMNs (P<0.10).

Conclusions

This pilot study highlights miRNAs that may aid in preoperative risk stratification of IPMNs and provides novel insights into miRNA-mediated progression to pancreatic malignancy. The miRNAs identified here and in other recent investigations warrant evaluation in biofluids in a well-powered prospective cohort of individuals newly-diagnosed with IPMNs and other pancreatic cysts and those at increased genetic risk for these lesions.     

Investigation on the potential application of biological agents in the extension of shelf life of fresh beef in Nigeria

The objective of this study was to evaluate the ability of lactic acid bacteria (LAB) cultures to preserve fresh beef at room temperature, with a view to promoting safety and availability of the product in Nigeria. Two LAB strains, Pediococcus pentosaceus LIV 01 and P. acidilactici FLE 01, were applied as starters (10⁶ cfu/g) on sliced fresh beef samples, and were stored for 7 days at 30°C. Analyses of microbiological, thiobarbituric acid (TBA) and free fatty acids (FFA) were carried out during storage. Results indicated reduction in the Enterobacteriaceae, Staphylococcus and coliforms in starter inoculated samples. TBA and FFA were lower in starter culture inoculated samples compared to controls during storage. In a challenge experiment against the LAB cultures during a 7-day storage, two sets of meat were inoculated separately with 10⁶ cfu/g each of pathogenic organisms Listeria monocytogenes and Salmonella Typhimurium. There was about 1 log reduction in the L. monocytogenes on day 1 while counts were below detection limit (<2 log) on day 2 in meat samples inoculated with P. pentosaceus alone and in combination with P. acidilactici. Counts of S. Typhimurium showed about 2 log reduction in starter inoculated samples during storage while an increase by about 3 log was observed in control samples. The protective ability of the LAB strains could be exploited in shelf life extension and control of foodborne pathogens in fresh beef; their use as biological preservatives may help in promoting public health, safety and availability of the product in Nigeria.