Mechanism of the plant cytochrome P450 for herbicide resistance: a modelling study

Curative anti-typhoid effect of Detarium microcarpum Guill. & Perr. (Leguminosae) hydroethanolic extract root bark based-on in vivo and molecular docking analyses

ETHNOPHARMACOLOGICAL RELEVANCE

Detarium microcarpum is used to treat typhoid fever, a major public health problem, by indigenous population in Africa. Though its preventive activities have been documented, the curative effect is still to be confirmed.

AIM OF THE STUDY

This study aimed at evaluating the curative effects of the hydroethanolic extract of Detarium microcarpum root bark on Salmonella typhimurium-induced typhoid in rat and exploring the in-silico inhibition of some bacterial key enzymes.

STUDY DESIGN

In vitro antioxydant, in vivo antisalmonella of the extract and in silico molecular docking assay on the isolated compounds were carried out to explore the anti-salmonella effects of Detarium microcarpum.

MATERIAL AND METHODS

The in vitro antioxidant properties of the extract were evaluated using DPPH, ABTS and FRAP tests. The anti-salmonella activity of the extract was assessed through feacal sample from Salmonella typhimurium-infected rat cultured in Salmonella-Shigella agar (SS agar) medium. The affinity of isolated compounds (Rhinocerotinoic acid and Microcarposide) from the extract were performed on four key enzymes (Adenylosuccinate lyase, Acetyl coenzyme A synthetase, Thymidine phosphorylase and LuxS-Quorum sensor) using molecular docking simulation to elucidate the molecular level inhibition mechanism.

RESULTS

Crude extract of D. microcarpum root bark showed variable activities on DPPH (RSa50: 6.09 ± 1.04 μg/mL), ABTS (RSa50: 24.46 ± 0.27), and FRAP (RSa50: 23.30 ± 0.23). The extract at all the doses exhibited significant healing effect of infected rats, with the complete clearance. The extract restored hematological, biochemical and histological parameters closed to the normal control. The molecular docking results indicates that rhinocerotinoic acid and microcarposide present more affinity to the LuxS-Quorum sensor and Acetyl coenzyme A synthetase protein as compared to the others.

CONCLUSION

These results demonstrate potent anti-typhoid activities of the hydroethanolic of Detarium microcarpum root bark extract through antioxidant properties and high inhibitory affinity of its compounds on some bacterial key enzymes that justify its use as traditional medicine to typhoid fever.

Mechanisms for the structural dependent transformation of 6:2 and 8:2 polyfluoroalkyl phosphate diesters in wheat (Triticum aestivum L.)

Polyfluoroalkyl phosphate esters (PAPs) are widely used and detected in various environmental media and organisms, but little is known about their behaviors in plants. In this study, the uptake, translocation and transformation of 6:2 and 8:2 diPAP in wheat using hydroponic experiments were investigated. 6:2 diPAP was more easily taken up by roots and translocated to shoots than 8:2 diPAP. Their phase I metabolites were fluorotelomer saturated carboxylates (FTCAs), fluorotelomer unsaturated carboxylates (FTUCAs) and perfluoroalkyl carboxylic acids (PFCAs). PFCAs with even-numbered chain length were the primary phase I terminal metabolites suggesting that they were mainly generated through β-oxidation. Cysteine and sulfate conjugates were the primary phase II transformation metabolites. The higher levels and ratios of phase II metabolites in the 6:2 diPAP exposure group indicated that the phase I metabolites of 6:2 diPAP were more susceptible to phase II transformation than that of 8:2 diPAP, which was confirmed by density functional theory calculation. Enzyme activity analyses and in vitro experiments demonstrated that cytochrome P450 and alcohol dehydrogenase actively participated in the phase Ⅰ transformation of diPAPs. Gene expression analyses showed that glutathione S-transferase (GST) was involved in the phase Ⅱ transformation, and the subfamily GSTU2 played a dominant role.

Sequence characterization of eccDNA content in glyphosate sensitive and resistant Palmer amaranth from geographically distant populations

The discovery of non-chromosomal circular DNA offers new directions in linking genome structure with function in plant biology. Glyphosate resistance through EPSPS gene copy amplification in Palmer amaranth was due to an autonomously replicating extra-chromosomal circular DNA mechanism (eccDNA). CIDER-Seq analysis of geographically distant glyphosate sensitive (GS) and resistant (GR) Palmer Amaranth (Amaranthus palmeri) revealed the presence of numerous small extra-chromosomal circular DNAs varying in size and with degrees of repetitive content, coding sequence, and motifs associated with autonomous replication. In GS biotypes, only a small portion of these aligned to the 399 kb eccDNA replicon, the vehicle underlying gene amplification and genetic resistance to the herbicide glyphosate. The aligned eccDNAs from GS were separated from one another by large gaps in sequence. In GR biotypes, the eccDNAs were present in both abundance and diversity to assemble into a nearly complete eccDNA replicon. Mean sizes of eccDNAs were similar in both biotypes and were around 5kb with larger eccDNAs near 25kb. Gene content for eccDNAs ranged from 0 to 3 with functions that include ribosomal proteins, transport, metabolism, and general stress response genetic elements. Repeat content among smaller eccDNAs indicate a potential for recombination into larger structures. Genomic hotspots were also identified in the Palmer amaranth genome with a disposition for gene focal amplifications as eccDNA. The presence of eccDNA may serve as a reservoir of genetic heterogeneity in this species and may be functionally important for survival.

Insight into Shenqi Jiangtang Granule on the improved insulin sensitivity by integrating in silico and in vivo approaches

ETHNOPHARMACOLOGICAL RELEVANCE

Presently, insulin resistance has been a growing concern that urgently needs to be addressed, because it not only places patients at risk of developing type 2 diabetes mellitus but also results in metabolic syndrome and different aspects of cardiovascular diseases. Shenqi Jiangtang Granule (SJG) is a classic traditional Chinese medicine (TCM) prescription that is widely used to treat diabetes mellitus and its complications in clinical practice. While studies have revealed that SJG with multi-ingredients and multi-targets characteristics possesses potential anti-insulin resistance pharmacological properties, its mechanisms of action and molecular targets for the treatment of insulin resistance are still obscure, which prompt us to conduct an in-depth research.

AIM OF THE STUDY

This study was purposed to uncover the pharmacological mechanism of SJG against insulin resistance through integrating network pharmacology and experimental validation.

MATERIALS AND METHODS

The putative ingredients of SJG and its related targets were discerned from the TCMSP database. Subsequently, insulin resistance-associated targets were retrieved from GeneCard, OMIM, and GEO database. Compound-target, protein-protein interaction (PPI), and compound-target-pathway networks were established using Cytoscape software. GO and KEGG pathway analyses were performed to identify possible enrichment of genes with specific biological themes. Molecular docking was used to verify the correlation between the main active ingredients and hub targets. Optimal docking conformation was further analyzed by molecular dynamics (MD) simulation. Finally, the potential molecular mechanisms of SJG acting on insulin resistance, as predicted by the network pharmacology analyses, were validated experimentally in insulin-resistant rat model.

RESULTS

136 active compounds, 211 corresponding targets in addition to 1463 disease-related targets were collected, of which 94 intersection targets were obtained. 29 key targets including AKT1, VEGFA, IL-6, CASP3, and PTGS2 were identified through PPI network analysis. Hub module of PPI network was closely associated with inflammation. GO and KEGG analyses also revealed that inflammation-related pathways may be a central factor for SJG to modulate insulin resistance. Molecular docking test showed a good binding potency between primary active ingredients and core targets, and the binding mode of optimal docking conformation was stable in MD simulation. A rat model of insulin resistance was successfully induced by chronic high-fat diet (HFD) consumption. Through a series of in vivo studies, including HEC, ITT, and HOMA-IR measurement, it was revealed that SJG exhibited a beneficial effect on ameliorating insulin resistance, as demonstrated by a significant increase of GIR and a significant decrease of AUCITT and HOMA-IR index value. Further molecular biological analysis showed that SJG can decrease the mRNA expression level and serum concentration of inflammatory cytokines (TNF-α, IL-6, and IL-1β), along with suppressing the p-NFκB protein overexpression, indicating its anti-inflammatory activity. Also, it can contribute to the reversal of the impaired hepatic insulin signaling pathway, as evidenced by up-regulated protein expression of p-Akt and GLUT2.

CONCLUSIONS

Through in silico and in vivo approaches, the present study not only provides a unique insight into the possible mechanism of SJG in insulin resistance after successfully filtering out associated key target genes and signaling pathways, but also suggests a novel promising therapeutic strategy for curing insulin resistance.

Insights into mechanisms involved in the uptake, translocation, and metabolism of phthalate esters in Chinese cabbage (Brassica rapa var. chinensis)

In the present study, the uptake and translocation mechanisms of phthalate esters (PAEs) and their primary mono esters metabolites (mPAEs), and the mechanisms of PAEs metabolism in plants were elucidated. The objectives of this study were to: (i) elucidate the fractionation of PAEs and mPAEs in Chinese cabbage (Brassica rapa var. chinensis) by hydroponic experiment, (ii) investigate the PAEs and mPAEs uptake mechanisms in root by inhibitor experiments, (iii) explain the molecular mechanisms of PAE interactions with the plant macromolecules by proteomics analysis and molecular docking, and (iv) reveal the involvement of carboxylesterase in the plant metabolism of PAEs. The results demonstrated that both the apoplastic and symplastic pathways contributed to the uptake of di-n-butyl phthalate (DnBP), di-(2-ethylhexyl) phthalate (DEHP), mono-n-butyl phthalate (MnBP), and mono-(2-ethylhexyl) phthalate (MEHP) by vacuum-infiltration-centrifugation method. The energy-dependent active process was involved for the uptake of DnBP, DEHP, MnBP, and MEHP. The passive uptake pathways of anion mPAEs and neutral PAEs differ. Aquaporins contributed to the uptake of anion MnBP and MEHP, and slow-type anion channel was also responsible for the uptake of anion MEHP. Molecular interactions of PAEs and macromolecules were further characterized by proteomic analysis and molecular docking. PAEs were transferred via non-specific lipid transfer protein by binding hydroponic amino acid residues. The carboxylesterase enzyme was attributed to the metabolism of PAEs to form mPAEs by using crude enzyme extract and commercial pure enzyme. This study provides both experimental and theoretical evidence for uptake, accumulation, and metabolism of PAEs in plants.

Optimisation of Cytochrome P450 BM3 Assisted by Consensus-Guided Evolution

Cytochrome P450 enzymes have attracted much interest over the years given their ability to insert oxygen into saturated carbon-hydrogen bonds, a difficult feat to accomplish by traditional chemistry. Much of the activity in this field has centered on the bacterial enzyme CYP102A1, or BM3, from Bacillus megaterium, as it has shown itself capable of hydroxylating/acting upon a wide range of substrates, thereby producing industrially relevant pharmaceuticals, fine chemicals, and hormones. In addition, unlike most cytochromes, BM3 is both soluble and fused to its natural redox partner, thus facilitating its use. The industrial use of BM3 is however stifled by its instability and its requirement for the expensive NADPH cofactor. In this work, we added several mutations to the BM3 mutant R966D/W1046S that enhanced the turnover number achievable with the inexpensive cofactors NADH and NBAH. These new mutations, A769S, S847G, S850R, E852P, and V978L, are localized on the reductase domain of BM3 thus leaving the oxidase domain intact. For NBAH-driven reactions by new mutant NTD5, this led to a 5.24-fold increase in total product output when compared to the BM3 mutant R966D/W1046S. For reactions driven by NADH by new mutant NTD6, this enhanced total product output by as much as 2.3-fold when compared to the BM3 mutant R966D/W1046S. We also demonstrated that reactions driven by NADH with the NTD6 mutant not only surpassed total product output achievable by wild-type BM3 with NADPH but also retained the ability to use this latter cofactor with greater total product output as well.

FastD: Fast detection of insecticide target-site mutations and overexpressed detoxification genes in insect populations from RNA-Seq data

Target-site mutations and detoxification gene overexpression are two major mechanisms conferring insecticide resistance. Molecular assays applied to detect these resistance genetic markers are time-consuming and with high false-positive rates. RNA-Seq data contains information on the variations within expressed genomic regions and expression of detoxification genes. However, there is no corresponding method to detect resistance markers at present. Here, we collected 66 reported resistance mutations of four insecticide targets (AChE, VGSC, RyR, and nAChR) from 82 insect species. Next, we obtained 403 sequences of the four target genes and 12,665 sequences of three kinds of detoxification genes including P450s, GSTs, and CCEs. Then, we developed a Perl program, FastD, to detect target-site mutations and overexpressed detoxification genes from RNA-Seq data and constructed a web server for FastD (http://www.insect-genome.com/fastd). The estimation of FastD on simulated RNA-Seq data showed high sensitivity and specificity. We applied FastD to detect resistant markers in 15 populations of six insects, Plutella xylostella, Aphis gossypii, Anopheles arabiensis, Musca domestica, Leptinotarsa decemlineata and Apis mellifera. Results showed that 11 RyR mutations in P. xylostella, one nAChR mutation in A. gossypii, one VGSC mutation in A. arabiensis and five VGSC mutations in M. domestica were found to be with frequency difference >40% between resistant and susceptible populations including previously confirmed mutations G4946E in RyR, R81T in nAChR and L1014F in VGSC. And 49 detoxification genes were found to be overexpressed in resistant populations compared with susceptible populations including previously confirmed detoxification genes CYP6BG1, CYP6CY22, CYP6CY13, CYP6P3, CYP6M2, CYP6P4 and CYP4G16. The candidate target-site mutations and detoxification genes were worth further validation. Resistance estimates according to confirmed markers were consistent with population phenotypes, confirming the reliability of this program in predicting population resistance at omics-level.

Herbicide Widespread: The Effects of Pethoxamid on Nonalcoholic Fatty Liver Steatosis In Vitro

Pethoxamid is a widespread herbicidal product, presenting itself as an extremely flexible active substance and with a high potential for use as an herbicide for preemergence. The emergence of multiple resistance in crops has been addressed using combinations of preemergence and postemergence herbicides in the same seeding-harvest cycle. A winning combination of pethoxamid and glyphosate mainly affected the acidobacteria population. Glyphosate scientific literature has demonstrated an observational link between herbicide exposure and liver disease in human subjects. Identifying and ranking the risk to the public that pethoxamid could exert on target organs has not been evaluated so far. Due to similarities to glyphosate, we did look at the effect of pethoxamid on impaired liver cells HepG2, using a nonalcoholic fatty liver disease (NAFLD) cell model in vitro. Pethoxamid was cytotoxic starting at 1 ppm. Fatty acid accumulation (FA) was enhanced while low doses of pethoxamid slightly decreased LDH protein expression compared to FA-treated HepG2. The same trend was observed for cytochrome c. Based on our data, we can argue that NAFLD hepatic cells react to pethoxamid trying detoxifying strategies, ready to undergo cell death to avoid further degeneration. Downregulation of cytochrome can lead to the hypothesis that pethoxamid should not induce herbicide resistance.

Measuring the structural impact of mutations on cytochrome P450 21A2, the major steroid 21-hydroxylase related to congenital adrenal hyperplasia

Congenital adrenal hyperplasia is an inherited autosomal recessive disorder related to deficient cortisol synthesis. The deficiency of steroid 21-hydroxylase (cytochrome P450 21A2), an enzyme involved in cortisol synthesis, is responsible for ∼95% of cases of congenital adrenal hyperplasia. This metabolic disease exhibits three clinical forms: salt-wasting, simple virilizing, and non-classical form, which are divided according to the degree of severity. In the present study, structural and mutational analyses were performed in order to identify the structural impact of mutations on cytochrome P450 21A2 and correlate them with patient clinical severity. The following mutations were selected: arginine-356 to tryptophan (R356W), proline-30 to leucine (P30L), isoleucine-172 to asparagine (I172N), valine-281 to leucine (V281L), and the null mutation glutamine-318 (Q318X). Our computational approach mapped the location of residues on P450 and identified their implications on enzyme electrostatic potential mapping to progesterone and heme binding pockets. Using molecular dynamics simulations, we analyzed the structural stability of ligand binding and protein structure, as well as possible conformational changes at the catalytic pocket that leads to impairment of enzymatic activity. Our study sheds light on the impact structural mutations have over steroid 21-hydroxylase structure-function in the cell.Communicated by Ramaswamy H. Sarma.

Uptake, Translocation, and Biotransformation of Organophosphorus Esters in Wheat (Triticum aestivum L.)

The uptake, translocation and biotransformation of organophosphate esters (OPEs) by wheat (Triticum aestivum L.) were investigated by a hydroponic experiment. The results demonstrated that OPEs with higher hydrophobicity were more easily taken up by roots, and OPEs with lower hydrophobicity were more liable to be translocated acropetally. A total of 43 metabolites including dealkylated, oxidatively dechlorinated, hydroxylated, methoxylated, and glutathione-, and glucuronide- conjugated products were detected derived from eight OPEs, with diesters formed by direct dealkylation from the parent triesters as the major products, followed with hydroxylated triesters. Molecular interactions of OPEs with plant biomacromolecules were further characterized by homology modeling combined with molecular docking. OPEs with higher hydrophobicity were more liable to bind with TaLTP1.1, the most important wheat nonspecific lipid transfer protein, consistent with the experimental observation that OPEs with higher hydrophobicity were more easily taken up by wheat roots. Characterization of molecular interactions between OPEs and wheat enzymes suggested that OPEs were selectively bound to TaGST4-4 and CYP71C6v1 with different binding affinities, which determined their abilities to be metabolized and form metabolite products in wheat. This study provides both experimental and theoretical evidence for the uptake, accumulation and biotransformation of OPEs in plants.

New strategies for overcoming limitations of mesenchymal stem cell-based immune modulation

Mesenchymal stem cells (MSCs) have rapidly been applied in a broad field of immune-mediated disorders since the first successful clinical use of MSCs for treatment of graft-versus-host disease. Despite the lack of supporting data, expectations that MSCs could potentially treat most inflammatory conditions led to rushed application and development of commercialized products. Today, both pre-clinical and clinical studies present mixed results for MSC therapy and the discrepancy between expected and actual efficacy of MSCs in various diseases has evoked a sense of discouragement. Therefore, we believe that MSC therapy may now be at a critical milestone for re-evaluation and re-consideration. In this review, we summarize the current status of MSC-based clinical trials and focus on the discrepancy between expected and actual outcome of MSC therapy from bench to bedside. Importantly, we discuss the underlying limitations of MSCs and suggest a new guideline for MSC therapy in hopes of improving their therapeutic efficacy.