Faculty Opinions recommendation of De novo biosynthesis of terminal alkyne-labeled natural products.

AbstractIsoflavonoids comprise a class of plant natural products with great nutraceutical, pharmaceutical and agricultural significance. Their low abundance in nature and structural complexity however hampers access to these phytochemicals through traditional crop-based manufacturing or chemical synthesis. Microbial bioproduction therefore represents an attractive alternative. Here, we engineer the metabolism of Saccharomyces cerevisiae to become a platform for efficient production of daidzein, a core chemical scaffold for isoflavonoid biosynthesis, and demonstrate its application towards producing bioactive glucosides from glucose, following the screening-reconstruction-application engineering framework. First, we rebuild daidzein biosynthesis in yeast and its production is then improved by 94-fold through screening biosynthetic enzymes, identifying rate-limiting steps, implementing dynamic control, engineering substrate trafficking and fine-tuning competing metabolic processes. The optimized strain produces up to 85.4 mg L−1 of daidzein and introducing plant glycosyltransferases in this strain results in production of bioactive puerarin (72.8 mg L−1) and daidzin (73.2 mg L−1). Our work provides a promising step towards developing synthetic yeast cell factories for de novo biosynthesis of value-added isoflavonoids and the multi-phased framework may be extended to engineer pathways of complex natural products in other microbial hosts.

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Partitioning Pattern of Natural Products Based on Molecular Properties Descriptors Representing Drug-Likeness

Symmetry ◽

10.3390/sym13040546 ◽

2021 ◽

Vol 13 (4) ◽

pp. 546

Author(s):

Miroslava Nedyalkova ◽

Vasil Simeonov

Keyword(s):

Natural Products ◽

Drug Discovery ◽

De Novo ◽

Target Prediction ◽

Natural Compounds ◽

Discovery Process ◽

Drug Discovery Process ◽

Unique Source ◽

The Times ◽

Partitioning Pattern

A cheminformatics procedure for a partitioning model based on 135 natural compounds including Flavonoids, Saponins, Alkaloids, Terpenes and Triterpenes with drug-like features based on a descriptors pool was developed. The knowledge about the applicability of natural products as a unique source for the development of new candidates towards deadly infectious disease is a contemporary challenge for drug discovery. We propose a partitioning scheme for unveiling drug-likeness candidates with properties that are important for a prompt and efficient drug discovery process. In the present study, the vantage point is about the matching of descriptors to build the partitioning model applied to natural compounds with diversity in structures and complexity of action towards the severe diseases, as the actual SARS-CoV-2 virus. In the times of the de novo design techniques, such tools based on a chemometric and symmetrical effect by the implied descriptors represent another noticeable sign for the power and level of the descriptors applicability in drug discovery in establishing activity and target prediction pipeline for unknown drugs properties.

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Identification of 3,4-Dihydro-2H,6H-pyrimido[1,2-c][1,3]benzothiazin-6-imine Derivatives as Novel Selective Inhibitors of Plasmodium falciparum Dihydroorotate Dehydrogenase

International Journal of Molecular Sciences ◽

10.3390/ijms22137236 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7236

Author(s):

Endah Dwi Hartuti ◽

Takaya Sakura ◽

Mohammed S. O. Tagod ◽

Eri Yoshida ◽

Xinying Wang ◽

...

Keyword(s):

Drug Target ◽

De Novo ◽

Dihydroorotate Dehydrogenase ◽

Chemical Library ◽

New Class ◽

De Novo Biosynthesis ◽

Starting Point ◽

Novel Drugs ◽

Low Toxicity ◽

Fourth Step

Plasmodium falciparum’s resistance to available antimalarial drugs highlights the need for the development of novel drugs. Pyrimidine de novo biosynthesis is a validated drug target for the prevention and treatment of malaria infection. P. falciparum dihydroorotate dehydrogenase (PfDHODH) catalyzes the oxidation of dihydroorotate to orotate and utilize ubiquinone as an electron acceptor in the fourth step of pyrimidine de novo biosynthesis. PfDHODH is targeted by the inhibitor DSM265, which binds to a hydrophobic pocket located at the N-terminus where ubiquinone binds, which is known to be structurally divergent from the mammalian orthologue. In this study, we screened 40,400 compounds from the Kyoto University chemical library against recombinant PfDHODH. These studies led to the identification of 3,4-dihydro-2H,6H-pyrimido[1,2-c][1,3]benzothiazin-6-imine and its derivatives as a new class of PfDHODH inhibitor. Moreover, the hit compounds identified in this study are selective for PfDHODH without inhibition of the human enzymes. Finally, this new scaffold of PfDHODH inhibitors showed growth inhibition activity against P. falciparum 3D7 with low toxicity to three human cell lines, providing a new starting point for antimalarial drug development.

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De novo Neurosteroidogenesis in Human Microglia: Involvement of the 18 kDa Translocator Protein

International Journal of Molecular Sciences ◽

10.3390/ijms22063115 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3115

Author(s):

Lorenzo Germelli ◽

Eleonora Da Pozzo ◽

Chiara Giacomelli ◽

Chiara Tremolanti ◽

Laura Marchetti ◽

...

Keyword(s):

Neurotrophic Factor ◽

De Novo ◽

Neuroactive Steroids ◽

Translocator Protein ◽

Compensatory Mechanism ◽

Human Microglia ◽

De Novo Biosynthesis ◽

Murine Microglia ◽

Synthetic Ligand ◽

Tspo Expression

Neuroactive steroids are potent modulators of microglial functions and are capable of counteracting their excessive reactivity. This action has mainly been ascribed to neuroactive steroids released from other sources, as microglia have been defined unable to produce neurosteroids de novo. Unexpectedly, immortalized murine microglia recently exhibited this de novo biosynthesis; herein, de novo neurosteroidogenesis was characterized in immortalized human microglia. The results demonstrated that C20 and HMC3 microglial cells constitutively express members of the neurosteroidogenesis multiprotein machinery—in particular, the transduceosome members StAR and TSPO, and the enzyme CYP11A1. Moreover, both cell lines produce pregnenolone and transcriptionally express the enzymes involved in neurosteroidogenesis. The high TSPO expression levels observed in microglia prompted us to assess its role in de novo neurosteroidogenesis. TSPO siRNA and TSPO synthetic ligand treatments were used to reduce and prompt TSPO function, respectively. The TSPO expression downregulation compromised the de novo neurosteroidogenesis and led to an increase in StAR expression, probably as a compensatory mechanism. The pharmacological TSPO stimulation the de novo neurosteroidogenesis improved in turn the neurosteroid-mediated release of Brain-Derived Neurotrophic Factor. In conclusion, these results demonstrated that de novo neurosteroidogenesis occurs in human microglia, unravelling a new mechanism potentially useful for future therapeutic purposes.

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Synthesis, utilization, and structure of the tetrahydropterin intermediates in the bovine adrenal medullary de novo biosynthesis of tetrahydrobiopterin.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)35846-5 ◽

1986 ◽

Vol 261 (6) ◽

pp. 2725-2737

Author(s):

G K Smith ◽

C A Nichol

Keyword(s):

De Novo ◽

De Novo Biosynthesis

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Epigenetic silencing of GTP cyclohydrolase 1 promotes hepatocellular carcinoma growth by activating superoxide anion-mediated ASK1/p38 signaling via inhibiting tetrahydrobiopterin de novo biosynthesis

Free Radical Biology and Medicine ◽

10.1016/j.freeradbiomed.2021.03.025 ◽

2021 ◽

Author(s):

Guo-Chao Zhong ◽

Zhi-Bo Zhao ◽

Yao Cheng ◽

Yun-Bing Wang ◽

Chan Qiu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Superoxide Anion ◽

De Novo ◽

Epigenetic Silencing ◽

Gtp Cyclohydrolase ◽

De Novo Biosynthesis

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Dietary Essential Amino Acid Restriction Promotes Hyperdipsia via Hepatic FGF21

Nutrients ◽

10.3390/nu13051469 ◽

2021 ◽

Vol 13 (5) ◽

pp. 1469

Author(s):

Patricia M. Rusu ◽

Andrea Y. Chan ◽

Mathias Heikenwalder ◽

Oliver J. Müller ◽

Adam J. Rose

Keyword(s):

Amino Acid ◽

Growth Factor ◽

Dietary Protein ◽

Essential Amino Acid ◽

De Novo ◽

Fibroblast Growth Factor 21 ◽

Fibroblast Growth ◽

De Novo Biosynthesis ◽

Dietary Requirements ◽

Dietary Amino Acid

Prior studies have reported that dietary protein dilution (DPD) or amino acid dilution promotes heightened water intake (i.e., hyperdipsia) however, the exact dietary requirements and the mechanism responsible for this effect are still unknown. Here, we show that dietary amino acid (AA) restriction is sufficient and required to drive hyperdipsia during DPD. Our studies demonstrate that particularly dietary essential AA (EAA) restriction, but not non-EAA, is responsible for the hyperdipsic effect of total dietary AA restriction (DAR). Additionally, by using diets with varying amounts of individual EAA under constant total AA supply, we demonstrate that restriction of threonine (Thr) or tryptophan (Trp) is mandatory and sufficient for the effects of DAR on hyperdipsia and that liver-derived fibroblast growth factor 21 (FGF21) is required for this hyperdipsic effect. Strikingly, artificially introducing Thr de novo biosynthesis in hepatocytes reversed hyperdipsia during DAR. In summary, our results show that the DPD effects on hyperdipsia are induced by the deprivation of Thr and Trp, and in turn, via liver/hepatocyte-derived FGF21.

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