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Computational Prediction and Experimental Validation of a Bridged Cation Intermediate in Akanthomycin Biosynthesis.

ABSTRACT: Here we report a computation-driven chemoenzymatic synthesis and biosynthesis of the natural product deoxyakanthomycin, an atropisomeric pyridone natural product that features a 7-membered carbocycle with five stereocenters, one of which a quaternary center. The one-step synthesis from a biosynthetic precursor is based on computational analysis that predicted a σ-bridged cation mediated cyclization mechanism to form deoxyakanthomycin. The σ-bridged cation rationalizes the observed substrate-controlled selectivity; diastereoselectivity arises from attack of water anti to the σ-bridging, as is generally found for σ-bridged cations. Our studies also reveal a unifying biosynthetic strategy for 2-pyridone natural products that derive from a common o-quinone methide to create diverse structures.

SUBMITTER: Jamieson CS

PROVIDER: S-EPMC9128357 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Computational Prediction and Experimental Validation of a Bridged Cation Intermediate in Akanthomycin Biosynthesis.

Jamieson Cooper S CS Ohashi Masao M Houk K N KN Tang Yi Y

Journal of the American Chemical Society 20220317 12

Here we report a computation-driven chemoenzymatic synthesis and biosynthesis of the natural product deoxyakanthomycin, an atropisomeric pyridone natural product that features a 7-membered carbocycle with five stereocenters, one of which a quaternary center. The one-step synthesis from a biosynthetic precursor is based on computational analysis that predicted a σ-bridged cation mediated cyclization mechanism to form deoxyakanthomycin. The σ-bridged cation rationalizes the observed substrate-cont ...[more]

PMID: 35297629

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Project description:Background: Alzheimer's disease (AD) is the major cause of dementia in population aged over 65 years, accounting up to 70% dementia cases. However, validated peripheral biomarkers for AD diagnosis are not available up to present. In this study, we adopted a new strategy of combination of computational prediction and experimental validation to identify blood protein biomarkers for AD. Methods: First, we collected tissue-based gene expression data of AD patients and healthy controls from GEO database. Second, we analyzed these data and identified differentially expressed genes for AD. Third, we applied a blood-secretory protein prediction program on these genes and predicted AD-related proteins in blood. Finally, we collected blood samples of AD patients and healthy controls to validate the potential AD biomarkers by using ELISA experiments and Western blot analyses. Results: A total of 2754 genes were identified to express differentially in brain tissues of AD, among which 296 genes were predicted to encode AD-related blood-secretory proteins. After careful analysis and literature survey on these predicted blood-secretory proteins, ten proteins were considered as potential AD biomarkers, five of which were experimentally verified with significant change in blood samples of AD vs. controls by ELISA, including GSN, BDNF, TIMP1, VLDLR, and APLP2. ROC analyses showed that VLDLR and TIMP1 had excellent performance in distinguishing AD patients from controls (area under the curve, AUC = 0.932 and 0.903, respectively). Further validation of VLDLR and TIMP1 by Western blot analyses has confirmed the results obtained in ELISA experiments. Conclusion: VLDLR and TIMP1 had better discriminative abilities between ADs and controls, and might serve as potential blood biomarkers for AD. To our knowledge, this is the first time to identify blood protein biomarkers for AD through combination of computational prediction and experimental validation. In addition, VLDLR was first reported here as potential blood protein biomarker for AD. Thus, our findings might provide important information for AD diagnosis and therapies.

Project description:BACKGROUND: In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their target genes has yet to be systematically characterized. We sought to elucidate a set of conserved miRNA/target-gene pairs and to analyse the mechanism underlying miRNA-mediated gene regulation in the early stage of bilaterian evolution. RESULTS: Initially, we extracted five evolutionarily conserved miRNAs (let-7, miR-1, miR-124, miR-125/lin-4, and miR-34) among five diverse bilaterian animals. Subsequently, we designed a procedure to predict evolutionarily conserved miRNA/target-gene pairs by introducing orthologous gene information. As a result, we extracted 31 orthologous miRNA/target-gene pairs that were conserved among at least four diverse bilaterian animals; the prediction set showed prominent enrichment of orthologous miRNA/target-gene pairs that were verified experimentally. Approximately 84% of the target genes were regulated by three miRNAs (let-7, miR-1, and miR-124) and their function was classified mainly into the following categories: development, muscle formation, cell adhesion, and gene regulation. We used a reporter gene assay to experimentally verify the downregulation of six candidate pairs (out of six tested pairs) in HeLa cells. CONCLUSIONS: The application of our new method enables the identification of 31 miRNA/target-gene pairs that were expected to have been regulated from the era of the common bilaterian ancestor. The downregulation of all six candidate pairs suggests that orthologous information contributed to the elucidation of the primordial set of genes that has been regulated by miRNAs; it was also an efficient tool for the elimination of false positives from the predicted candidates. In conclusion, our study identified potentially important miRNA-target pairs that were evolutionarily conserved throughout diverse bilaterian animals and that may provide new insights into early-stage miRNA functions.

Dataset Information

Computational Prediction and Experimental Validation of a Bridged Cation Intermediate in Akanthomycin Biosynthesis.

Publications

Computational Prediction and Experimental Validation of a Bridged Cation Intermediate in Akanthomycin Biosynthesis.

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