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1.
Acta Crystallogr C Struct Chem ; 80(Pt 2): 43-48, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38281183

ABSTRACT

Cedrol-like compounds are of pharmacological interest due to their diverse range of medicinal effects and are used globally in traditional medicines and cosmetics. Many cedrol tautomers are known from molecular studies but few have been studied in crystalline form by X-ray diffraction. Acicular white crystals collected from the wood of eastern red cedar (Juniperus virginiana) are determined to be (+)-cedrol hemihydrate, namely, (1S,2R,5S,7R,8R)-2,6,6,8-tetramethyltricyclo[5.3.1.01,5]undecan-8-ol hemihydrate, C15H26O·0.5H2O, a novel packing of two unique cedrol molecules (Z' = 2) with a single water molecule [space group P212121; a = 6.1956 (1), b = 14.5363 (1), and c = 30.9294 (4) Å]. The hydrogen bonding forms a one-dimensional spiral chain running along the a axis, following the chirality of the cedrol molecule, through hydrogen-bonding interactions with a right-handed helical configuration in graph-set notation Δ-C33(6) > a > c > b. The crystal packing and symmetry are different from crystalline isocedrol due to the different hydrogen-bonding geometry.

2.
Structure ; 32(2): 200-216.e5, 2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38157857

ABSTRACT

Phosphorylation of the σ54-dependent transcription activator FlrC by the sensor histidine kinase FlrB is essential for flagellar synthesis of Vibrio cholerae. Despite that, the structure, sensory signal, and mechanistic basis of function of FlrB were elusive. Here, we report the crystal structure of the sensory PAS domain of FlrB in its functional dimeric state that exhibits a unique architecture. Series of biochemical/biophysical experiments on different constructs and mutants established that heme binds hydrophobically as sensory ligand in the shallow ligand-binding cleft of FlrB-PAS without axial coordination. Intriguingly, ATP binding to the C-terminal ATP-binding (CA) domain assists PAS domain to bind heme, vis-à-vis, heme binding to the PAS facilitates ATP binding to the CA domain. We hypothesize that synergistic binding of heme and ATP triggers conformational signaling in FlrB, leading to downstream flagellar gene transcription. Enhanced swimming motility of V. cholerae with increased heme uptake supports this proposition.


Subject(s)
Bacterial Proteins , Heme , Bacterial Proteins/chemistry , Histidine Kinase/genetics , Ligands , Adenosine Triphosphate
3.
J Hazard Mater ; 465: 133287, 2024 03 05.
Article in English | MEDLINE | ID: mdl-38141318

ABSTRACT

Microorganisms play a critical role in the biogeochemical cycling of selenium, often reducing selenite/selenate to elemental selenium nanoparticles (SeNPs). These SeNPs typically exist in an amorphous structure but can transform into a trigonal allotrope. However, the crystal structural transition process and its impact on selenium bioavailability have not been well studied. To shed light on this, we prepared chemosynthetic and biogenic SeNPs and investigated the stability of their crystal structure. We found that biogenic SeNPs exhibited a highly stable amorphous structure in various conditions, such as lyophilization, washing, and laser irradiation, whereas chemosynthetic SeNPs transformed into a trigonal structure in the same conditions. Additionally, a core-shell structure was observed in biogenic SeNPs after electron beam irradiation. Further analysis revealed that biogenic SeNPs showed a coordination reaction between Se atoms and surface binding biomacromolecules, indicating that the outer layer of Se-biomacromolecules complex prevented the SeNPs from crystallizing. We also investigated the effects of SeNPs crystal structures on the bioavailability in bacteria, yeast, and plants, finding that the amorphous structure of SeNPs determined Se bioavailability.


Subject(s)
Nanoparticles , Selenium , Selenium/metabolism , Biological Availability , Nanoparticles/chemistry , Antioxidants/metabolism , Oxidation-Reduction
4.
Appl Environ Microbiol ; 89(10): e0118523, 2023 10 31.
Article in English | MEDLINE | ID: mdl-37791757

ABSTRACT

Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel ß-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.


Subject(s)
Alginates , Bacteria , Humans , Alginates/metabolism , Bacteria/metabolism , Oligosaccharides/metabolism , Polysaccharide-Lyases/metabolism , Substrate Specificity
5.
Molecules ; 28(11)2023 May 24.
Article in English | MEDLINE | ID: mdl-37298774

ABSTRACT

The aim of the research described in this publication is two-fold. The first is a detailed description of the synthesis of a series of compounds containing a stereogenic heteroatom, namely the optically active P-stereogenic derivatives of tert-butylarylphoshinic acids bearing sulfur or selenium. The second is a detailed discussion dedicated to the determination of their structures by an X-ray analysis. Such a determination is needed when considering optically active hetero-oxophosphoric acids as new chiral solvating agents, precursors of new chiral ionic liquids, or ligands in complexes serving as novel organometallic catalysts.


Subject(s)
Organometallic Compounds , Selenium , Organometallic Compounds/chemistry , Crystallography, X-Ray , Stereoisomerism
6.
J Agric Food Chem ; 71(22): 8471-8478, 2023 Jun 07.
Article in English | MEDLINE | ID: mdl-37230944

ABSTRACT

The amino acids l-arginine and l-ornithine are widely used in animal feed and as health supplements and pharmaceutical compounds. In arginine biosynthesis, acetylornithine aminotransferase (AcOAT) uses pyridoxal-5'-phosphate (PLP) as a cofactor for amino group transfer. Here, we determined the crystal structures of the apo and PLP complex forms of AcOAT from Corynebacterium glutamicum (CgAcOAT). Our structural observations revealed that CgAcOAT undergoes an order-to-disorder conformational change upon binding with PLP. Additionally, we observed that unlike other AcOATs, CgAcOAT exists as a tetramer. Subsequently, we identified the key residues involved in PLP and substrate binding based on structural analysis and site-directed mutagenesis. This study might provide structural insights on CgAcOAT, which can be utilized for the development of improved l-arginine production enzymes.


Subject(s)
Corynebacterium glutamicum , Corynebacterium glutamicum/metabolism , Transaminases/genetics , Mutagenesis, Site-Directed , Arginine , Crystallography, X-Ray
7.
Proc Natl Acad Sci U S A ; 120(11): e2220677120, 2023 03 14.
Article in English | MEDLINE | ID: mdl-36888659

ABSTRACT

Control over transition metal redox state is essential for metalloprotein function and can be achieved via coordination chemistry and/or sequestration from bulk solvent. Human methylmalonyl-Coenzyme A (CoA) mutase (MCM) catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA using 5'-deoxyadenosylcobalamin (AdoCbl) as a metallocofactor. During catalysis, the occasional escape of the 5'-deoxyadenosine (dAdo) moiety leaves the cob(II)alamin intermediate stranded and prone to hyperoxidation to hydroxocobalamin, which is recalcitrant to repair. In this study, we have identified the use of bivalent molecular mimicry by ADP, coopting the 5'-deoxyadenosine and diphosphate moieties in the cofactor and substrate, respectively, to protect against cob(II)alamin overoxidation on MCM. Crystallographic and electron paramagnetic resonance (EPR) data reveal that ADP exerts control over the metal oxidation state by inducing a conformational change that seals off solvent access, rather than by switching five-coordinate cob(II)alamin to the more air stable four-coordinate state. Subsequent binding of methylmalonyl-CoA (or CoA) promotes cob(II)alamin off-loading from MCM to adenosyltransferase for repair. This study identifies an unconventional strategy for controlling metal redox state by an abundant metabolite to plug active site access, which is key to preserving and recycling a rare, but essential, metal cofactor.


Subject(s)
Molecular Mimicry , Vitamin B 12 , Humans , Oxidation-Reduction , Adenosine Diphosphate/metabolism , Vitamin B 12/metabolism , Methylmalonyl-CoA Mutase/chemistry , Methylmalonyl-CoA Mutase/metabolism
8.
Acta Crystallogr D Struct Biol ; 79(Pt 2): 188-197, 2023 Feb 01.
Article in English | MEDLINE | ID: mdl-36762864

ABSTRACT

Secretory phospholipase A2 (sPLA2), which hydrolyzes the sn-2 acyl bond of lecithin in a Ca2+-dependent manner, is an important enzyme in the oil and oleochemical industries. However, most sPLA2s are not stable under process conditions. Therefore, a thermostable sPLA2 was investigated in this study. A marine bacterial sPLA2 isolated from Sciscionella marina (Sm-sPLA2) was catalytically active even after 5 h of incubation at high temperatures of up to 50°C, which is outstanding compared with a representative bacterial sPLA2 (i.e. sPLA2 from Streptomyces violaceoruber; Sv-sPLA2). Consistent with this, the melting temperature of Sm-sPLA2 was measured to be 7.7°C higher than that of Sv-sPLA2. Furthermore, Sm-sPLA2 exhibited an improved biotransformation performance compared with Sv-sPLA2 in the hydrolysis of soy lecithin to lysolecithin and free fatty acids at 50°C. Structural and mutagenesis studies revealed that the Trp41-mediated anchoring of a Ca2+-binding loop into the rest of the protein body is directly linked to the thermal stability of Sm-sPLA2. This finding provides a novel structural insight into the thermostability of sPLA2 and could be applied to create mutant proteins with enhanced industrial potential.


Subject(s)
Liposomes , Phospholipases A2, Secretory , Lecithins , Hydrolysis
9.
Acta Pharmacol Sin ; 44(6): 1217-1226, 2023 Jun.
Article in English | MEDLINE | ID: mdl-36650291

ABSTRACT

Retinoic-acid-receptor-related orphan receptor γ (RORγ) is a major transcription factor for proinflammatory IL-17A production. Here, we revealed that the RORγ deficiency protects mice from STZ-induced Type 1 diabetes (T1D) through inhibiting IL-17A production, leading to improved pancreatic islet ß cell function, thereby uncovering a potential novel therapeutic target for treating T1D. We further identified a novel RORγ inverse agonist, ginseng-derived panaxadiol, which selectively inhibits RORγ transcriptional activity with a distinct cofactor recruitment profile from known RORγ ligands. Structural and functional studies of receptor-ligand interactions reveal the molecular basis for a unique binding mode for panaxadiol in the RORγ ligand-binding pocket. Despite its inverse agonist activity, panaxadiol induced the C-terminal AF-2 helix of RORγ to adopt a canonical active conformation. Interestingly, panaxadiol ameliorates mice from STZ-induced T1D through inhibiting IL-17A production in a RORγ-dependent manner. This study demonstrates a novel regulatory function of RORγ with linkage of the IL-17A pathway in pancreatic ß cells, and provides a valuable molecule for further investigating RORγ functions in treating T1D.


Subject(s)
Diabetes Mellitus, Type 1 , Panax , Animals , Mice , Interleukin-17/metabolism , Diabetes Mellitus, Type 1/chemically induced , Diabetes Mellitus, Type 1/drug therapy , Ligands , Drug Inverse Agonism , Panax/metabolism , Nuclear Receptor Subfamily 1, Group F, Member 3/agonists
10.
Nat Prod Res ; 37(1): 68-76, 2023 Jan.
Article in English | MEDLINE | ID: mdl-34498960

ABSTRACT

A new icetexane diterpenoid, 11, 12, 20α-trihydroxyl-7ß-methoxyicetexa-8, 11, 13-triene-19, 10-lactone [Phyllane A (1)], and a new abietane diterpenoid, 7ß, 20-epoxy-3ß, 17-acetoxy-abieta-8, 11, 13-teriene-11, 12-diol [phyllane B (2)], along with two known compounds (3 and 4) were isolated from the methanol (MeOH) extract of twigs and leaves of the folk medicinal Isodon phyllopodus. Their structures were determined by spectroscopic analyses including 2 D NMR spectral data, and further confirmed by X-ray single crystal diffraction. Moreover, the compounds were evaluated for their cytotoxicity and anti-HIV activities, and phyllane A showed anti-HIV activity with an IC50 value of 15.7 µM, but phyllane B was found to be cytotoxic to the A549 host cells with a CC50 value of 108.5 µM.


Subject(s)
Antineoplastic Agents, Phytogenic , Diterpenes , Isodon , Abietanes/pharmacology , Abietanes/chemistry , Isodon/chemistry , Antineoplastic Agents, Phytogenic/chemistry , Diterpenes/chemistry , Plant Leaves/chemistry , Molecular Structure
11.
Adv Mater ; 35(8): e2207945, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36448300

ABSTRACT

Consolidating a microscopic understanding of magnetic properties is crucial for a rational design of magnetic materials with tailored characteristics. The interplay of 3d and 4f magnetism in rare-earth transition metal antimonides is an ideal platform to search for such complex behavior. Here the synthesis, crystal growth, structure, and complex magnetic properties are reported of the new compound Pr3 Fe3 Sb7 as studied by magnetization and electrical transport measurements in static and pulsed magnetic fields up to 56 T, powder neutron diffraction, and Mößbauer spectroscopy. On cooling without external magnetic field, Pr3 Fe3 Sb7 shows spontaneous magnetization, indicating a symmetry breaking without a compensating domain structure. The Fe substructure exhibits noncollinear ferromagnetic order below the Curie temperature TC  ≈ 380 K. Two spin orientations exist, which approximately align along the Fe-Fe bond directions, one parallel to the ab plane and a second one with the moments canting away from the c axis. The Pr substructure orders below 40 K, leading to a spin-reorientation transition (SRT) of the iron substructure. In low fields, the Fe and Pr magnetic moments order antiparallel to each other, which gives rise to a magnetization antiparallel to the external field. At 1.4 K, the magnetization approaches saturation above 40 T. The compound exhibits metallic resistivity along the c axis, with a small anomaly at the SRT.

12.
Int J Pharm ; 630: 122458, 2023 Jan 05.
Article in English | MEDLINE | ID: mdl-36462740

ABSTRACT

Alzheimer's disease (AD) is a devastating neurodegenerative disease caused by multiple factors. Single-target drugs have limited efficacy for AD treatment. Therefore, multi-target intervention strategy has great potential. Traditional Chinese medicine (TCM) is mostly used in the form of compound prescription, which has the polypharmacology behavior. Rhizoma Coptidis and Radix et Rhizoma Rhei are frequently used as the couplet medicines of TCM for AD therapy. In this study, the novel carrier-free nanoassembly with 3D-porous frame crystal structure has formulated from supramolecular self-assembly of berberine (BER) and rhein (RHE), the main active components of Rhizoma Coptidis and Radix et Rhizoma Rhei, respectively. Combining with the spectral data and single crystal structure, the self-assembly process was clarified as dominated by electrostatic interaction and π-π stacking. In vitro release property, cholinesterase (ChE) inhibition, ß-amyloid (Aß) aggregation regulation, radical elimination, metal ions chelation and cytotoxicity assay indicated that the obtained BER-RHE assembly had the Fickian diffusion-controlled sustained release ability, synergistic biological activities and virtually no neurotoxicity. In addition, in vivo reactive oxygen species (ROS) level evaluation showed that the assembly could reduce the accumulation of intracellular ROS in Caenorhabditis elegans (C. elegans). Meanwhile, BER-RHE assembly could also be used as a novel potential carrier for drug delivery due to its superior 3D-porous frame. This green and facile strategy for carrier-free nanoassembly microscopic construction via supramolecular self-assembly might provide inspiration for the development of multi-target therapy for AD and the design of the novel drug delivery system.


Subject(s)
Alzheimer Disease , Berberine , Drugs, Chinese Herbal , Neurodegenerative Diseases , Animals , Humans , Alzheimer Disease/drug therapy , Berberine/chemistry , Caenorhabditis elegans , Drugs, Chinese Herbal/chemistry , Porosity , Reactive Oxygen Species , Rhizome
13.
Med Chem ; 19(2): 174-192, 2023.
Article in English | MEDLINE | ID: mdl-35993458

ABSTRACT

INTRODUCTION: An analysis of the literature on the painkillers long used in traditional medicine, which are isolated from plant materials, has shown that many of them are alkylamides of various carboxylic acids. This fact served as the basis for the study of a large group of N-alkyl-4- methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxamides as potential new analgesics. The objects of the study were synthesized in the traditional way involving the initial conversion of 4-methyl- 2,2-dioxo-1H-2λ6,1- benzothiazine-3-carboxylic acid to imidazolide, in which imidazolide was used as an acylating agent. The method is simple to implement and, as a rule, gives high yields of final alkylamides. However, in reaction with sterically hindered tert-butylamine, along with the "normal" product, an unexpected formation of N-tert-butyl-4-methyl-1-(4-methyl-2,2-dioxo-1H-2λ6,1- benzothiazine-3-carbonyl)-2,2-dioxo-2λ6,1-benzothiazine-3-carboxamide was observed, which was characterized by X-ray diffraction analysis as a monosolvate with N,N-dimethylformamide. These synthetic problems can be avoided using a more powerful acylating agent, 4-methyl-2,2-dioxo-1H- 2λ6,1- benzothiazine-3-carbonyl chloride. BACKGROUND: A large group of new N-alkyl-4-methyl-2,2-dioxo-1H-2λ6,1-benzothiazine-3- carboxamides was synthesized. OBJECTIVE: On the basis of molecular docking, some derivatives of N-alkyl-4-methyl-2,2-dioxo-1H- 2λ6,1-benzothiazine-3-carboxamides have been designed. Their preliminary structure-activity relationships (SAR) have been studied. The most rational approaches to the synthesis of lead compounds have been developed. The most active compounds have shown high anti-inflammatory and analgesic activities. METHODS: The structure of all compounds prepared has been confirmed by the data of elemental analysis, 1H- and 13C NMR spectroscopy, and electrospray ionization liquid chromato-mass spectrometry. For rational drug design, optimization of further pharmacological screening and prediction of a possible mechanism of pharmacological action, molecular docking has been performed. For the determination of activity, pharmacological studies have been carried out. RESULTS: Pharmacological tests have determined that the transition from N-aryl(heteroaryl) alkylamides to "pure" N-alkylamides we carried out is accompanied by a significant reduction and even complete loss of anti-inflammatory effect with remaining analgesic activity. CONCLUSION: According to the studies, compounds from N-alkyl-4-methyl-2,2-dioxo-1H-2λ6,1- benzothiazine-3-carboxamides are potential anti-inflammatory and analgesic agents.


Subject(s)
Analgesics , Anti-Inflammatory Agents , Molecular Docking Simulation , Analgesics/pharmacology , Analgesics/chemistry , Anti-Inflammatory Agents/pharmacology , Structure-Activity Relationship , Indicators and Reagents/pharmacology
14.
Food Res Int ; 162(Pt A): 111933, 2022 12.
Article in English | MEDLINE | ID: mdl-36461191

ABSTRACT

The formation of starch-lipid complexes in instant rice noodles (IRN) free from and incorporated with fatty acids (FAs) and their impacts on textural, in vitro digestive and retrogradation properties were investigated. The gelatinization enthalpy values of IRN samples (1.24-4.93 J/g) were noticeably decreased (P < 0.05) compared to rice starch samples (2.54-6.89 J/g) fortified with FAs. Additionally, long-chain saturated FAs (stearic acid (SA, C18:0)) complexes produced higher ordered structures than the shorter-chain FAs (C12:0-C16:0), for 18-carbon FAs, the unsaturated FAs (linoleic acid (LOA, C18:2)) exhibited the strongest intermolecular interactions with rice starch. The relative crystallinity of IRN (27.01%-38.47%) was lower than the rice starch-FAs complexes (38.36%-56.80%). FAs delayed the retrogradation degree of IRN storaged at 4 °C for 21 days ascribed to the formation of V-type complexes. Higher enzymatic resistance was observed in IRN added FAs with resistant starch content increased from 5.13% to 14.42% (LOA), and the sample fortified with SA exhibited the highest slowly digestible starch content (35.92%). SEM revealed that the IRN compounded with palmitic acid, SA and LOA displayed more compact and regular structures. Overall, the formation of starch-FAs complexes probably is a novel strategy in improving the textural, digestive, and retrogradation properties of IRN.


Subject(s)
Oryza , Starch , Fatty Acids , Digestion , Dietary Supplements
15.
Pharmaceutics ; 14(11)2022 Nov 16.
Article in English | MEDLINE | ID: mdl-36432669

ABSTRACT

Dehydroepiandrosterone (DHEA) is an FDA-approved food supplement used as an assisted reproductive sex hormone. The bioavailability is severely limited by its poor solubility (23 µg/mL). Herein, we aimed to modulate its solubility through cocrystallization. Eight cocrystals of DHEA with pyrocatechol (CAT), hydroquinone (HQ), resorcinol (RES), phloroglucinol (PG), 1,5-dihydroxy naphthalene (DHN), p-hydroxybenzoic acid (PHBA), gallic acid (GA), and 5-hydroxyisophthalic acid (5HIPA) were designed and synthesized. Some basic characterization tools, including powder X-ray diffraction, thermogravimetric analysis, differential scanning calorimetry, and Fourier transform infrared spectroscopy, were also applied in our work for basic analyses of cocrystals. It is indicated that DHEA-GA exhibits its superiority in dissolution and pharmacokinetic behaviors. While the area under the curve values of DHEA-GA is improved at the ratio of 2.2, the corresponding bioavailability of DHEA is expected to be accordingly increased.

16.
BMC Biol ; 20(1): 217, 2022 10 05.
Article in English | MEDLINE | ID: mdl-36199108

ABSTRACT

BACKGROUND: Nuclear receptors are transcription factors of central importance in human biology and associated diseases. Much of the knowledge related to their major functions, such as ligand and DNA binding or dimerization, derives from functional studies undertaken in classical model animals. It has become evident, however, that a deeper understanding of these molecular functions requires uncovering how these characteristics originated and diversified during evolution, by looking at more species. In particular, the comprehension of how dimerization evolved from ancestral homodimers to a more sophisticated state of heterodimers has been missing, due to a too narrow phylogenetic sampling. Here, we experimentally and phylogenetically define the evolutionary trajectory of nuclear receptor dimerization by analyzing a novel NR7 subgroup, present in various metazoan groups, including cnidarians, annelids, mollusks, sea urchins, and amphioxus, but lost in vertebrates, arthropods, and nematodes. RESULTS: We focused on NR7 of the cephalochordate amphioxus B. lanceolatum. We present a complementary set of functional, structural, and evolutionary analyses that establish that NR7 lies at a pivotal point in the evolutionary trajectory from homodimerizing to heterodimerizing nuclear receptors. The crystal structure of the NR7 ligand-binding domain suggests that the isolated domain is not capable of dimerizing with the ubiquitous dimerization partner RXR. In contrast, the full-length NR7 dimerizes with RXR in a DNA-dependent manner and acts as a constitutively active receptor. The phylogenetic and sequence analyses position NR7 at a pivotal point, just between the basal class I nuclear receptors that form monomers or homodimers on DNA and the derived class II nuclear receptors that exhibit the classical DNA-independent RXR heterodimers. CONCLUSIONS: Our data suggest that NR7 represents the "missing link" in the transition between class I and class II nuclear receptors and that the DNA independency of heterodimer formation is a feature that was acquired during evolution. Our studies define a novel paradigm of nuclear receptor dimerization that evolved from DNA-dependent to DNA-independent requirements. This new concept emphasizes the importance of DNA in the dimerization of nuclear receptors, such as the glucocorticoid receptor and other members of this pharmacologically important oxosteroid receptor subfamily. Our studies further underline the importance of studying emerging model organisms for supporting cutting-edge research.


Subject(s)
Receptors, Glucocorticoid , Receptors, Retinoic Acid , Animals , DNA , Dimerization , Humans , Ketosteroids , Ligands , Phylogeny , Receptors, Cytoplasmic and Nuclear/genetics , Receptors, Glucocorticoid/genetics , Receptors, Retinoic Acid/chemistry , Receptors, Retinoic Acid/genetics , Receptors, Retinoic Acid/metabolism , Retinoid X Receptors/chemistry , Retinoid X Receptors/genetics , Retinoid X Receptors/metabolism
17.
Acta Crystallogr D Struct Biol ; 78(Pt 10): 1273-1282, 2022 Oct 01.
Article in English | MEDLINE | ID: mdl-36189746

ABSTRACT

The bacterial nitroreductases (NRs) NfsB and NfsA are conserved homodimeric FMN-dependent flavoproteins that are responsible for the reduction of nitroaromatic substrates. Berberine (BBR) is a plant-derived isoquinoline alkaloid with a large conjugated ring system that is widely used in the treatment of various diseases. It was recently found that the gut microbiota convert BBR into dihydroberberine (dhBBR, the absorbable form) mediated by bacterial NRs. The molecular basis for the transformation of BBR by the gut microbiota remains unclear. Here, kinetic studies showed that NfsB from Escherichia coli (EcNfsB), rather than EcNfsA, is responsible for the conversion of BBR to dhBBR in spite of a low reaction rate. The crystal structure of the EcNfsB-BBR complex showed that BBR binds into the active pocket at the dimer interface, and its large conjugated plane stacks above the plane of the FMN cofactor in a nearly parallel orientation. BBR is mainly stabilized by π-stacking interactions with both neighboring aromatic residues and FMN. Structure-based mutagenesis studies further revealed that the highly conserved Phe70 and Phe199 are important residues for the conversion of BBR. The structure revealed that the C6 atom of BBR (which receives the hydride) is ∼7.5 Šfrom the N5 atom of FMN (which donates the hydride), which is too distant for hydride transfer. Notably, several well ordered water molecules make hydrogen-bond/van der Waals contacts with the N1 atom of BBR in the active site, which probably donate protons in conjunction with electron transfer from FMN. The structure-function studies revealed the mechanism for the recognition and binding of BBR by bacterial NRs and may help to understand the conversion of BBR by the gut microbiota.


Subject(s)
Berberine , Escherichia coli Proteins , Bacteria/metabolism , Carbon-Oxygen Ligases/metabolism , Escherichia coli/metabolism , Flavin Mononucleotide/chemistry , Flavoproteins/metabolism , Isoquinolines , Kinetics , Medicine, Traditional , Nitroreductases/chemistry , Nitroreductases/metabolism , Protons , Water
18.
J Hazard Mater ; 435: 129022, 2022 08 05.
Article in English | MEDLINE | ID: mdl-35500348

ABSTRACT

A major environmental concern related to nuclear energy is wastewater contaminated with uranium, thus necessitating the development of pollutant-reducing materials with efficiency and effectiveness. Herein, highly selective mesoporous silicas functionalized with amine-bridged diacetamide ligands SBA-15-ABDMA were prepared. Different spectroscopy techniques were used to probe the chemical environment and reactivity of the chelating ligands before and after sorption. The results showed that the functionalized SBA-15-ABDMA had a strong affinity for uranium at low pH (pH = 3) with desirable sorption capacity (68.82 mg/g) and good reusability (> 5). It showed excellent separation performance with a high distribution coefficient (Kd,U > 105 mL/g) and separation factors SFU/Ln > 1000 at a pH of 3.5 in the presence of lanthanide nuclides, alkaline earth metal and transition metal ions. In particular, SiO2spheres-ABDMA was used as a column material, which achieved excellent recovery of U(VI) (> 98%) and good reusability for samples of simulated mining and nuclear industries wastewater. XPS and crystallography studies clearly illustrated the tridentate coordination mode of U(VI)/PEABDMA and the mechanism and origin behind the high selectivity for U.


Subject(s)
Uranium , Adsorption , Amines , Ligands , Silicon Dioxide/chemistry , Uranium/chemistry , Wastewater
19.
Int J Biol Macromol ; 209(Pt A): 1271-1279, 2022 Jun 01.
Article in English | MEDLINE | ID: mdl-35460754

ABSTRACT

Inhibiting α-glucosidase activity is important in controlling postprandial hyperglycemia and, thus, helping to manage type-2 diabetes mellitus (T2DM). In the present study, we purified a hypothetical protein of carrots called DCHP (Daucus Carrot hypoglycemic peptide), and their inhibitory effects on α-glucosidase, as well as related mechanisms, were investigated. The recombinant DCHP protein with a molecular weight of 8 kDa showed strong inhibitory activity against α-glycosidase and maintained good stability in solution. DCHP exhibited no inhibitory activity but was tolerant to trypsin and chymotrypsin. Cellular experiments demonstrated that glucose consumption and lactic acid production increased rapidly when treated with DCHP in Caco-2 and HepG2 cells. DCHP crystal was generated, and the crystal structure, which was similar to that of rBTI and consisted of a central α-helix and a two-stranded ß-sheet with a unique loop region. The interaction between DCHP and α-glycosidase was investigated by molecular docking and site-directed mutation, which revealed that Glu43, Pro46, Thr47 Thr48 and Gln49 are the key residues in DCHP that inhibit α-glycosidase activity. This work provides potential bioactive peptides as functional foods or nutraceutical supplements in preventing and managing T2DM.


Subject(s)
Daucus carota , Diabetes Mellitus, Type 2 , Caco-2 Cells , Diabetes Mellitus, Type 2/drug therapy , Glycoside Hydrolase Inhibitors/chemistry , Glycoside Hydrolase Inhibitors/pharmacology , Glycoside Hydrolases , Humans , Hypoglycemic Agents/pharmacology , Molecular Docking Simulation , Peptide Hydrolases , Protease Inhibitors , alpha-Glucosidases/metabolism
20.
Mol Divers ; 26(2): 1077-1100, 2022 Apr.
Article in English | MEDLINE | ID: mdl-33988806

ABSTRACT

Mono-/dispirocyclotriphosphazenes with pendant arm(s) are robust, but they are less investigated inorganic ring systems. In this study, a series of mono (3 and 4)- and dispirocyclotriphosphazenes with 4-chloro-benzyl pendant arm(s) (13-16) was obtained from the Cl exchange reactions of hexachlorocyclotriphosphazene with sodium (N-benzyl)aminopropanoxides (1 and 2). When compound (3) reacted with excess pyrrolidine, morpholine, tetra-1,4-dioxa-8-azaspiro[4,5]decane (DASD) and piperidine, the fully substituted monospirocyclotriphosphazenes (7, 9, 10 and 12) occurred. But, the reactions of 4 with excess piperidine and morpholine produced the gem-piperidino (5)- and morpholino (6)-substituted monospirocyclotriphosphazenes, whereas the reactions of 4 with excess pyrrolidine and DASD gave the fully substituted monospirocyclotriphosphazenes (8) and (11). However, it should be indicated that these derivatives were obtained to be used for the investigation of their spectral, stereogenic and biological properties. The structures of 5, 7 and 14 were determined crystallographically. X-ray data of 5 and 14 displayed that both of compounds were chiral in solid state, and their absolute configurations were assigned as R and RR. Additionally, the antimicrobial activities of phosphazenes were investigated. Minimum inhibitory concentrations, minimal bacterial concentrations and minimum fungicidal concentrations of phosphazenes were determined. The interactions of phosphazenes with plasmid DNA were evaluated by agarose gel electrophoresis. The cytotoxic activities of compounds were studied against L929 fibroblast and DLD-1 colon cancer cells. In addition, density functional theory calculations of 5, 7 and 14 were reported, and their molecular docking studies with DNA, E. coli DNA gyrase and topoisomerase IV were presented.


Subject(s)
Anti-Infective Agents , Antineoplastic Agents , Anti-Bacterial Agents/chemistry , Anti-Infective Agents/chemistry , Antineoplastic Agents/chemistry , Crystallography, X-Ray , DNA/chemistry , Escherichia coli , Microbial Sensitivity Tests , Molecular Docking Simulation , Morpholines , Nitrogen/chemistry , Nitrogen Compounds/chemistry , Nitrogen Compounds/pharmacology , Phosphorus/chemistry , Piperidines , Pyrrolidines/pharmacology
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