IMN4NPD: An Integrated Molecular Networking Workflow for Natural Product Dereplication.

Molecular networking has emerged as a standard approach for natural product (NP) discovery. However, the current pipeline based on molecular networks tends to prioritize larger clusters comprising multiple nodes. To address this issue, we present the integrated molecular networking workflow for NP dereplication (IMN4NPD). This approach not only expedites the rapid dereplication of extensive clusters within the molecular network but also places specific emphasis on self-looped or pairs of nodes, which are often overlooked by the current methods. By amalgamating the outputs from various computational tools, we efficiently dereplicate compounds falling into specific categories and provide annotations for both large cluster nodes and self-looped or pair of nodes within the molecular network. Furthermore, we have incorporated several fundamentally distinct similarity algorithms, namely, Spec2Vec and MS2DeepScore, for constructing the t-SNE network. Through comparison with modified cosine similarity, we have observed that integrating additional diverse spectral similarity measures, the resulting t-SNE network enhanced the ability to dereplicate NPs. Demonstrating the use case of an ethanol extract of Plumula nelumbinis, we illustrate that an integration of multiple computational solutions with IMN4NPD aids the dereplication, especially self-looped nodes, and in the discovery of novel compounds in NPs.

Nontargeted screening method for detection of illicit adulterants in dietary supplements and herbal medicines using UHPLC-QTOF-MS with fine-tuned Spec2Vec-based spectral similarity and chemical classification filter.

Liquid chromatography-mass spectrometry (LC-MS) is a widely utilized technique for inspecting adulteration. Unscrupulous businesses persistently introduce novel illegal adulterants, making it necessary to develop methods to screen compounds not present in the current library. Conventional cosine similarity for mass spectral libraries matching is limited in their ability to identify structurally similar compounds. In our previous study, comparison of performance among four advanced similarity algorithms revealed that Spec2Vec exhibited the best performance in terms of both detection capability and false discovery rate, making it the chosen method for identifying illegal adulterants. However, Spec2Vec still exhibited worse performance compared to MS2DeepScore and entropy similarity in the aspects of detection capability and false discovery rate, respectively. In this study, our objective was to optimize the performance of spectral similarity for a specific compound class by fine-tuning a pretrained Spec2Vec model. Additionally, we implemented the chemical classification tool CANOPUS to address the issue of similarities in backbone structures between illegal adulterants and compounds found in herbal medicine, which can lead to false positives. We utilized glucocorticoids as potentially illicit adulterants to provide a proof-of-concept, and the results demonstrated that the fine-tuned Spec2Vec model not only exhibits a significant improvement in detection ability compared to the original model but also achieves comparable performance to MS2Deepscore. Moreover, the fine-tuned Spec2Vec model shows notably fewer false positives in comparison to MS2Deepscore. Overall, this proposed pipeline demonstrates high effectiveness and competitiveness in inspecting illegal adulterants, enhancing the analysis of large-scale MS data.

Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries.

Despite extensive research on the gut microbiome of healthy individuals from a single country, there are still a limited number of population-level comparative studies. Moreover, the sequencing approach used in most related studies involves 16 S ribosomal RNA (rRNA) sequencing with a limited resolution, which cannot provide detailed functional profiles. In the present study, we applied a combined analysis approach to analyze whole metagenomic shotgun sequencing data from 2035 healthy adult samples from six countries across four continents. Analysis of core species revealed that 13 species were present in more than 90 % of all investigated individuals, the majority of which produced short-chain fatty acids (SCFA)-producing bacteria. Our analysis revealed consistently significant differences in gut microbial species and pathways between Western and non-Western countries, such as Escherichia coli and the relation of MetaCyc pathways to the TCA cycle. Specific changes in microbial species and pathways are potentially related to lifestyle and diet. Furthermore, we identified several noteworthy microbial species and pathways that exhibit distinct characteristics specific to China. Interestingly, we observed that China (CHN) was more similar to the United States (USA) and United Kingdom (GBR) in terms of the taxonomic and functional composition of the gut microbiome than India (IND) and Madagascar (MDG), which were more similar to the China (CHN) diet. The current study identified consistent microbial features associated with population and geography, which will inspire further clinical translations that consider paying attention to differences in microbiota backgrounds and confounding factors.

Fast screening and identification of illegal adulteration in dietary supplements and herbal medicines using molecular networking with deep-learning-based similarity algorithms.

Liquid chromatography-high-resolution mass spectrometry (LC-HRMS) is a powerful analytical tool used for adulteration inspection. Nevertheless, it is a challenging task to identify illegal adulterants that are not included in the library or are unexpected from large MS data. Molecular networking is a good tool for exploring, visualizing, and organizing MS/MS spectra, and moreover, it employs shifted peak match to calculate spectral similarity, making it capable of identifying adulteration that is not included in the library. The key of molecular networking is spectral similarity algorithms, and therefore, in this study, we compared the performance of four cutting-edge similarity algorithms, modified cosine similarity (shifted peak match), entropy similarity, and two deep-learning-based algorithms, MS2DeepScore and Spec2Vec, in building molecular networking for identification of adulteration that is not included in the library. We conducted an analysis of excluded-query-compound on all MS/MS spectra in test library and performed a large-scale false discovery rate estimation to investigate whether the spectral similarity calculated by each algorithm could represent the actual structural similarity well. The obtained results demonstrated Spec2Vec exhibited good performance in both detection capability and false discovery rate. Further comprehensive evaluation of the performance of Spec2Vec in the identification of adulteration that is not included in the library or is unexpected in different matrices and in application to real samples proved the approach studied here is a promising and powerful tool for adulterant inspection and improved the capability of analyzing large MS data.

Fast Screening and Identification of Illegal Adulterated Glucocorticoids in Dietary Supplements and Herbal Products Using UHPLC-QTOF-MS With All-Ion Fragmentation Acquisition Combined With Characteristic Fragment Ion List Classification.

Ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) with all-ion fragmentation (AIF) acquisition was established for an identification and quantification of illegal adulterated glucocorticoids in dietary supplements and herbal products. Next, a novel method called characteristic fragment ion list classification (CFILC) was developed for a fast screening of adulterated compounds. CFILC could provide the characteristic ions comprehensively and completely through direct extract from the MS2 library instead of finding them manually. This is time-saving and provides fast screening results with a high confidence level by filtering of a pre-calculated threshold of similarity scores for illegal adulterants that are not included in the library as well as for new emerging structural analogs. The obtained results demonstrated the great qualitative and quantitative strength of this approach, providing a promising and powerful method for a routine fast screening of illegal adulterated glucocorticoids.

Pharmacist impact on adherence of valproic acid therapy in pediatric patients with epilepsy using active education techniques.

There is limited information on the impact of active education by a pharmacist in the population of pediatric patients with epilepsy (PWE) in China. The objective of this study was to assess the effect of education by pharmacists on medication adherence and percentage of valproic acid (VPA) samples reaching therapeutic reference range in these patients. This study was conducted at two teaching hospitals in Changsha, China. Patients were retrospectively identified from January 2016 to December 2017. Active education by a pharmacist in both oral and written formats was provided at the intervention hospital whereas standard passive pharmacist service (dispensing and answering questions) was provided at the control hospital. Medication adherence was assessed by the simplified medication adherence questionnaire (SMAQ), and serum concentrations of VPA were collected. The correlation between pharmacist education and medication adherence and percentage of VPA samples reaching therapeutic reference range were analyzed. A total of 2165 patients and 4343 serum VPA concentrations were included in the analysis. For the first therapeutic drug monitoring (TDM) measurement, there was no statistical difference between the two hospitals: 41.3% of VPA samples reached therapeutic range at the intervention hospital compared with 45.4% at the control hospital (χ2 = 3.686, P > 0.05). After pharmacist intervention at the intervention hospital, however, there were significant differences in the percentage of therapeutic VPA samples reaching therapeutic range between the first and the second, third, fourth, and fifth TDM measurements (χ2 = 9.756, P < 0.01; χ2 = 22.840, P < 0.01; χ2 = 15.816, P < 0.01; χ2 = 27.613, P < 0.01). Based on the SMAQ adherence assessment, adherence increased from a minimum of 56.0% to a maximum of 73.9% with stabilization during the last six months of follow-up at the intervention hospital. Both the medication adherence rate and the percentage of VPA samples reaching therapeutic range increased as the result of active education by a pharmacist, suggesting that continuous pharmacist intervention had a positive impact in outpatient pediatric PWE.

High-throughput determination of vancomycin in human plasma by a cost-effective system of two-dimensional liquid chromatography.

Therapeutic drug monitoring (TDM) is one of the most important services of clinical laboratories. Two main techniques are commonly used: the immunoassay and chromatography method. We have developed a cost-effective system of two-dimensional liquid chromatography with ultraviolet detection (2D-LC-UV) for high-throughput determination of vancomycin in human plasma that combines the automation and low start-up costs of the immunoassay with the high selectivity and sensitivity of the liquid chromatography coupled with mass spectrometric detection without incurring their disadvantages, achieving high cost-effectiveness. This 2D-LC system offers a large volume injection to provide sufficient sensitivity and uses simulated gradient peak compression technology to control peak broadening and to improve peak shape. A middle column was added to reduce the analysis cycle time and make it suitable for high-throughput routine clinical assays. The analysis cycle time was 4min and the peak width was 0.8min. Compared with other chromatographic methods that have been developed, the analysis cycle time and peak width for vancomycin was reduced significantly. The lower limit of quantification was 0.20µg/mL for vancomycin, which is the same as certain LC-MS/MS methods that have been recently developed and validated. The method is rapid, automated, and low-cost and has high selectivity and sensitivity for the quantification of vancomycin in human plasma, thus making it well-suited for use in hospital clinical laboratories.

First Analysis of the Association Between CYP3A4/5, ABCB1 Genetic Polymorphisms and Oxcarbazepine Metabolism and Transport in Chinese Epileptic Patients with Oxcarbazepine Monotherapy and Bitherapy.

PURPOSE: Oxcarbazepine (OXC) is widely used in anti-epileptic treatment. Cytochrome P450 3A4 (CYP3A4), cytochrome P450 3A5(CYP3A5), and ATP-binding cassette sub-family B member 1 (ABCB1) are potential genes involved in OXC metabolisms and transport in vivo. This study aims to examine the genetic effects of CYP3A4, CYP3A5, and ABCB1 on OXC metabolism and transport in Chinese epileptic patients using OXC as monotherapy and bitherapy with lamotrigine (LTG), levetiracetam (LEV), or valproic acid (VPA). METHODS: Sixty-six Chinese epileptic patients were recruited from Xiangya Hospital Central South University, of whom 40 patients were receiving OXC monotherapy, 11 patients were placed in the OXC bitherapy group combined with one enzyme-inducing anti-epileptic drugs (LTG or LEV), and 15 patients were placed in the OXC bitherapy group combined with VPA. Oxcarbazepine and its main metabolite 10-hydrocarbazepine (MHD) plasma concentrations were measured using high performance liquid chromatography (HPLC)-UV method. In addition, eight single nucleotide polymorphisms (SNPs) in CYP3A4, CYP3A5, ABCB1 gene were genotyped by polymerase chain reaction-improved multiple ligase detection reaction (PCR-iMLDR). RESULTS: In the OXC+VPA group, ABCB1 rs2032582 and rs2032582-rs10234411-rs1045642 TAG haplotype were associated with MHD and MHD+OXC plasma concentration before permutation test. In OXC monotherapy and OXC+ LTG/LEV groups, no significant association between genetic polymorphisms in CYP3A4/5, ABCB1 gene and OXC plasma concentration parameters were observed. CONCLUSION: CYP3A4/5 and ABCB1 genetic variants might not take part in the metabolism and transport of MHD and OXC among epileptic patients using OXC monotherapy and bitherapy in combination with LEV, LTG or VPA.

Effects of CYP3A4/5 and ABCB1 genetic polymorphisms on carbamazepine metabolism and transport in Chinese patients with epilepsy treated with carbamazepine in monotherapy and bitherapy.

OBJECTIVE: To examine the effects of cytochrome P450 3A4 (CYP3A4), cytochrome P450 3A5 (CYP3A5) and ATP-binding cassette sub-family B member 1 (ABCB1) genetic polymorphisms on carbamazepine (CBZ) plasma concentrations in Chinese patients with epilepsy using CBZ as monotherapy and bitherapy with phenytoin (PHT), phenobarbital (PB), or valproic acid (VPA). METHODS: Eighty-eight Chinese patients with epilepsy were recruited from Xiangya Hospital Central South University, of whom 66 patients were placed in the CBZ monotherapy group, 10 patients were placed in the CBZ bitherapy group combined with one enzyme-inducing anti-seizure medications (PHT or PB), and 12 patients were placed in the CBZ bitherapy group combined with VPA. Carbamazepine and carbamazepine-10,11-epoxide (CBZ-E) plasma concentration of these patients were measured. In addition, the genetic polymorphisms of rs4646440 and rs2242480 in the CYP3A4 gene, rs15524 and rs776746 in the CYP3A5 gene, and rs1045642, rs2032582, rs10234411 and rs1128503 in the ABCB1 gene of the cohort were genotyped. Subsequently, the associations between CBZ plasma concentrations and target single-nucleotide polymorphisms (SNPs), as well as haplotypes, were analysed. RESULTS: In the CBZ monotherapy group, dose-adjusted CBZ concentrations were not associated with the eight SNPs and haplotypes. In the CBZ+PHT/PB group, rs776746, rs15524 and rs15524-rs776746 GT, AC haplotype were significantly associated with dose-adjusted CBZ plasma concentration (P=0.006, 0.006, 0.003, 0.003, respectively) and CBZ plus CBZ-E concentrations (P=0.006, 0.006, 0.006, 0.006, respectively); rs2032582, rs10234411 and rs2032582-rs10234411 AT, and CA haplotype were associated with the CBZ-E/CBZ ratio (P=0.007, 0.004, 0.004, 0.007, respectively). CONCLUSIONS: rs776746 and rs15524 in the CYP3A5 gene tend to affect CBZ metabolism, and rs2032582, rs10234411 in the ABCB1 gene may contribute to inter-individual variation in CBZ and in CBZ-E transport among patients with epilepsy using CBZ in combination with PHT or PB.

Association between two functional SNPs of SCN1A gene and efficacy of carbamazepine monotherapy for focal seizures in Chinese Han epileptic patients.

OBJECTIVE: To investigate whether single nucleotide polymorphisms (SNPs) of rs2298771 and rs3812718 of the sodium channel α-subunit type 1 (SCN1A) gene affect the efficacy of carbamazepine (CBZ) treatment for seizures in Chinese Han epileptic patients. METHODS: SNP rs2298771 and rs3812718 of the SCN1A gene from 628 patients were genotyped. CBZ monotherapy was administered to the subjects with new-onset partial seizures. The efficacy was defined as the decrease in the number of seizures. Four semi-quantitative levels were used to assess the efficacy: seizure-free (SF), >75% seizure decrease (SD), 50%-75% SD, and <50% SD in the number of seizures compared with patients' initial conditions. RESULTS: After the 12 month treatment with CBZ monotherapy, the rate of SF patients with G allele of the SNP rs2298771 was significantly lower than that in patients with the AA genotype (P=0.003). The heterozygote and homozygote of the G allele at SNP rs2298771 predicted the low SF rate (OR=2.101, 95% CI 1.289-3.425). Marginal significance was observed between the dichotomous efficacy of SF and non-SF in 3 partial seizure types (P=0.028). CONCLUSION: rs2298771 is significantly associated with the efficacy of CBZ monotherapy in Chinese Han epileptic patients.