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Probing the selectivity of urea, amide, and amine-based EPHX2 inhibitors towards EPHX1 and EPHX3: A computational study
No full textEpoxyeicosatrienoic acids (EETs) are crucial lipid signaling molecules that exert anti-inflammatory, vasodilatory,
and cardioprotective effects. While their therapeutic potential is limited due to rapid degradation mediated
primarily by soluble epoxide hydrolase (EPHX2). To address this, EPHX2 inhibitors having urea, amide, and
amine-based compounds have been developed to enhance EET bioavailability. However, their selectivity profiles
against other isoforms (EPHX1 and EPHX3) remain poorly characterized, raising concerns about potential off-
target effects, particularly the disruption of EPHX1’s xenobiotic detoxification function. Through computa-
tional approach involving molecular docking, and dynamics simulations, we systematically investigated the
evaluation of inhibitor binding preferences in relation to experimentally reported IC50 values. We found that
urea-based inhibitors showed slightly better affinity for EPHX3 followed by EPHX2, with generally lower binding
to EPHX1 except for specific compounds like t-TUCB, t-AUCB, and R-Talinolol that exhibited similar binding
affinity. Amide inhibitors preferentially bound EPHX3 through a stabilizing flip conformation (with Ad-APCA
demonstrating strongest binding), while amine inhibitors showed comparable affinities across all isoforms.
These findings are based on the relative binding energy trends derived from modelled catalytic domain which
highlight the critical influence of active site sub-pocket nature and its interactions and conformational adapt-
ability on inhibitor selectivity. Further capturing the structural dynamics and entropy of membrane anchoring of
EPHX3 and solvent exposure difference provide clues for structure-guided development of EPHX2 and EPHX3
isoform specific inhibitors to maximize therapeutic efficacy while minimizing interference with other physio-
logically important epoxide hydrolases
MksEF Accessory Proteins Inhibit MksB ATPase Activity and Modulate DNA Substrate Binding
No full textChromosome organization and segregation are
fundamental processes across all domains of life. In bacteria, the
mechanisms governing nucleoid organization remain poorly under-
stood. This study investigates the function of an alternative structural
maintenance of chromosomes (SMC) complex, MksBEF, in
Mycobacterium smegmatis. We show that MksB, the SMC subunit of
the complex, binds DNA and plays a crucial role in local chromosome
organization, a function distinct from that of other condensins. We
successfully reconstituted the MksBEF complex and determined its
stoichiometry as MksB2E4F2 using gel filtration and ultracentrifuga-
tion. Gel shift assays and isothermal titration calorimetry reveal that
the accessory proteins MksE and MksF interact with MksB and
significantly enhance its DNA-binding affinity�an effect not
observed in SMC or MukB-associated accessory proteins. Furthermore, ANS-based fluorescence experiments indicate that DNA
binding induces structural rearrangements in both MksB alone and the MksBEF complex. Notably, although MksEF enhances the
DNA-binding affinity of MksB, it also markedly suppresses its ATPase activity, a unique regulatory mechanism distinct from other
SMC complexes. These findings provide mechanistic insights into how MksE and MksF modulate MksB activity, advancing our
understanding of chromosome dynamics in mycobacteria
Quantification of water-soluble synthetic colors by HPLC-DAD method
No full textA simple yet accurate liquid chromatography method has been developed for the simultaneous quantitative determination of food colorants in a few commercially available foods. This analysis method incorporates an easy-to-follow extraction process with water as the extraction solvent to achieve the best color extraction. A Newcrom BH column with isocratic elution was employed for the analysis, and the components of the mobile phase were methanol, water, and sulphuric acid. To increase the sensitivity for analyte determination, color additives were quantified using multiple specific wavelengths. All 4 synthetic colour compounds (INS 102, INS 110, INS 129 & INS 133) showed good linearity with coefficient of determination above 0.999. This quick and easy technique enables the simultaneous determination of four artificial colorants in food products with recoveries averaging 87% among the examined food commodities and a minimum quantification range from 2.0 mg/kg
Geochemical Settings at an Alkaline Hydrothermal Vent Stabilized Ribose: Evidence from Chemical Garden and Other Simulation Experiments
No full textThe origin of life is an unsolved mystery. The
discovery of a hydrothermal vent starting from black smoke to a
lost city has sparked a spotlight on a hydrothermal vent as the place
of origin of life having all the prerequisite settings including a
proton gradient, thermal energy, mineral catalysts, and simple
constituent molecules for the emergence of life. On the other hand,
the RNA world hypothesis, which is an offshoot of the primordial
soup theory, presupposes ribose availability and its stability as the
primary milestone for abiotic synthesis of RNA. We demonstrate
through chemical garden and other simulation experiments
stabilization of ribose under a geochemical setting of deep ocean
hydrothermal vents occurring via acidic ocean water interaction
with brucite and calcite chimneys. The early Earth scenario,
wherein boric acid-containing seawater interacts with hydrothermal vent materials such as CaCO3, Mg(OH)2, and Ca(OH)2 along
with ribose, has been modeled utilizing chemical garden and prebiotic simulation experiments (NMR scale as well as synthetic
scale). The performed experiments reveal formation of metal borate, and its subsequent role in stabilization of ribose is
demonstrated via concrete evidence consisting of FT-IR, 1H NMR, and 11B NMR spectra
Whole Genome Analysis of Limosilactobacillus fermentum MCC0552 for Probiotic Functionalities and Comparative Genomic Study with Reference Strains
No full textLimosilactobacillus fermentum MCC0552, a potential probiotic was isolated from a dairy source. L. fermentum MCC0552
has been proven earlier to enhance immuno-modulatory response by alleviating inflammatory and diabetic effects. The
objective of this study is to analyse the whole genome sequence of L. fermentum MCC0552 for probiotic functionalities and
to compare it with the reference strains. The general genomic features of L. fermentum strain MCC0552 were analysed and a
phylogenetic dendrogram was generated by considering the genome sequences of reference strains (L. fermentum IFO 3956,
F-6, MTCC 5898 and ATCC 14931 or B1 28) which elucidates their evolutionary lineage. Functional analysis of MCC0552
reveals that the strain possess vitamin biosynthesis gene (thiamine and riboflavin) and mucin binding protein (mubp) with
comparatively larger in size. HPLC analysis suggests that the strain MCC0552 synthesises class B vitamins (B1, B2, B6,
B9 and B12) which increases its significance in nutritional and nutraceutical applications. Genomic island (GI) prediction
shows 19 GI in strain MCC0552 genome were identified. GI regions possessed CRISPR cluster genes, mainly type IE, cas2
and type III-A, nucleotide sugar biosynthesis gene, TA system genes, heavy metal associated genes, etc. On further analysis,
the strain exhibited the presence of 2 intact prophage regions which ensure its supplementary probiotic attribute. Thus, the
present study elaborates on the probiotic potential of strain MCC0552 at the genome level, revealing its remarkable genomic
potential and presenting novel prospects for utilising its unique genetic features in diverse scientific fields
Identification of tropolone derivatives from black turmeric (Curcuma caesia Roxb.) essential oil and their application in postharvest management of mangoes (Mangifera indica L.)
No full textThe present study focused on the identification of tropolone derivatives in the essential oils of black turmeric (Curcuma caesia Roxb.). Cyclohepta[b]furan-2-ones and azulene compounds to which tropolone might be the precursor were detected in the essential oils. Predominant compounds present were curzerenone (51.11–70.26%), curzerene (1.85–3.62%), germacrone (3.64–12.54%) and eremanthin (3.9–5.08%). The efficacy of extracted essential oil (BTC) and tropolone (TC) on postharvest quality of edible coated mangoes was studied during storage at 28 ± 2 °C (RT) and 9 ± 2 °C (LT).
Treated mangoes showed lower water loss and higher firmness
than control mangoes at both temperatures. β-carotene and sugar content increased in the mangoes stored at RT indicating ripening with higher TSS (Total Soluble Solids) and lower acidity (p < 0.05). Phenolic and flavonoid concentration was retained in the coated mangoes at LT. The study concluded that the BTC and TC mangoes at LT extended the shelf life with delayed ripening
