Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode

Novel Techniques and Models for Studying the Role of the Gut Microbiota in Drug Metabolism

The gut microbiota, known as the second human genome, plays a vital role in modulating drug metabolism, significantly impacting therapeutic outcomes and adverse effects. Emerging research has elucidated that the microbiota mediates a range of modifications of drugs, leading to their activation, inactivation, or even toxication. In diverse individuals, variations in the gut microbiota can result in differences in microbe-drug interactions, underscoring the importance of personalized approaches in pharmacotherapy. However, previous studies on drug metabolism in the gut microbiota have been hampered by technical limitations. Nowadays, advances in biotechnological tools, such as microbially derived metabolism screening and microbial gene editing, have provided a deeper insight into the mechanism of drug metabolism by gut microbiota, moving us toward personalized therapeutic interventions. Given this situation, our review summarizes recent advances in the study of gut-microbiota-mediated drug metabolism and showcases techniques and models developed to navigate the challenges posed by the microbial involvement in drug action. Therefore, we not only aim at understanding the complex interaction between the gut microbiota and drugs and outline the development of research techniques and models, but we also summarize the specific applications of new techniques and models in researching gut-microbiota-mediated drug metabolism, with the expectation of providing new insights on how to study drug metabolism by gut microbiota.

Adsorption-precipitation-cross-linking immobilization of GDSL-type esterase from Aspergillus niger GZUF36 by polydopamine-modified magnetic clarity tetroxide nanocouplings and its enzymatic characterization

Recombinant INANE1 (rINANE1), a recombinant intracellular GDSL-type esterase from Aspergillus niger GZUF36, has high acetate substrate specificity. Here, rINANE1 was successfully immobilized on polydopamine (PDA)-modified magnetic ferric oxide nanoparticles (Fe₃O₄NPs) by adsorption-precipitation-cross-linking to obtain cross-linked enzyme aggregate (CLEA)-rINANE1-Fe₃O₄@PDA. Fe₃O₄, Fe₃O₄@PDA, and CLEA-rINANE1-Fe₃O₄@PDA were characterized by scanning electron microscopy, X-ray diffraction, vibrating-sample magnetometry, Fourier transform infrared (FTIR) spectroscopy, and zeta potential analysis. Upon immobilization, CLEA-rINANE1-Fe₃O₄@PDA, with a protein loading of 72.72 ± 1.01 mg/g, reached optimal activity recovery of 104.40 % ± 1.14 %. FTIR analysis showed that immobilization increased the relative content of β-folding in rINANE1 by 12.25 % and reduced irregular curl by 4.16 %, rendering the structure more orderly. Specifically, under an alkaline condition (pH 10), CLEA-rINANE1-Fe₃O₄@PDA performed over 100 % of initial activity. The optimum temperature increased by 5 °C, and over 55 % of the initial activity was observed after 12 h at 55 °C. CLEA-rINANE1-Fe₃O₄@PDA showed over 40 % of its relative activity, whereas free rINANE1 showed <10 % in acetonitrile. In addition, the relative activity of CLEA-rINANE1-Fe₃O₄@PDA was retained at about 80 % after eight cycles and maintained at 109 % after 45 days. The PDA-modified magnetic ferrite nanoparticles exhibited excellent stability and recyclability, providing a new avenue for developing industrial biocatalysts.

Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages

Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.

RRLC-QTOF/MS-Based Metabolomics Reveal the Mechanism of Chemical Variations and Transformations of Astragali Radix as a Result of the Roasting Process

Astragali Radix (AR), which is extensively used as a healthy food supplement and medicinal herb, contains two forms of products corresponding to raw Astragalus Radix (RAR) and processed Astragali Radix (PAR), which was obtained by roasting. In this study, a non-targeted rapid resolution liquid chromatography coupled with quadruple time-of-flight mass spectrometry (RRLC-Q/TOF-MS) based metabolomics approach was developed to investigate the chemical changes of AR due to roasting. A total of 63 compounds were identified or tentatively identified. Among them, 23 isoflavonoids (composed of 12 isoflavones, eight pterocarpans, and three isoflavans) and six cycloastragenols were characterized as differential metabolites. Heatmap visualization and high-performance liquid chromatography coupled with photodiode array and evaporative light scattering detector (HPLC–PDA-ELSD) quantitative analysis revealed that malonyl isoflavonoids or cycloastragenols were at higher levels in RAR. These might be converted to corresponding acetyl isoflavonoids and cycloastragenols and related isoflavonoid glycosides during roasting. To prove this prediction, chemical conversion experiments on malonyl isoflavonoids and cycloastragenols were performed to confirm and clarify the chemical transformation mechanism.

Pharmacomicrobiomics: Exploiting the Drug-Microbiota Interactions in Antihypertensive Treatment

Hypertension is a leading risk factor for cardiovascular diseases and can reduce life expectancy. Owing to the widespread use of antihypertensive drugs, patients with hypertension have improved blood pressure control over the past few decades. However, for a considerable part of the population, these drugs still cannot significantly improve their symptoms. In order to explore the reasons behind, pharmacomicrobiomics provide unique insights into the drug treatment of hypertension by investigating the effect of bidirectional interaction between gut microbiota and antihypertensive drugs. This review discusses the relationship between antihypertensive drugs and the gut microbiome, including changes in drug pharmacokinetics and gut microbiota composition. In addition, we highlight how our current knowledge of antihypertensive drug-microbiota interactions to develop gut microbiota-based personalized ways for disease management, including antihypertensive response biomarker, microbial-targeted therapies, probiotics therapy. Ultimately, a better understanding of the impact of pharmacomicrobiomics in the treatment of hypertension will provide important information for guiding rational clinical use and individualized use.

Rational Design for Broadened Substrate Specificity and Enhanced Activity of a Novel Acetyl Xylan Esterase from Bacteroides thetaiotaomicron

Gut bacteria-derived enzymes play important roles in the metabolism of dietary fiber through enabling the hydrolysis of polysaccharides. In this study, we identified and characterized a 29 kDa novel acetyl xylan esterase, BTAxe1, from Bacteroides thetaiotaomicron VPI5482. Then, we solved the structure of BTAxe1 and performed the rational design. Mutants N65S and N65A increased the activities toward short-chain (pNPA, pNPB) to near four-fold, and gained the activities toward longer-chain substrate (pNPO). Molecular docking analysis showed that the mutant N65S had a larger substrate binding pocket than the wild type. Hydrolysis studies using natural substrates showed that either N65S or N65A showed higher activity of that of wild-type, yielding 131.31 and 136.09 mM of acetic acid from xylan. This is the first study on the rational design of gut bacteria-derived Axes with broadened substrate specificity and enhanced activity, which can be referenced by other acetyl esterases or gut-derived enzymes.