Academic literature on the topic 'Synthetic pathway biotransformation'
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Journal articles on the topic "Synthetic pathway biotransformation"
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Zhang, Y.-H. Percival, Jibin Sun, and Jian-Jiang Zhong. "Biofuel production by in vitro synthetic enzymatic pathway biotransformation." Current Opinion in Biotechnology 21, no. 5 (October 2010): 663–69. http://dx.doi.org/10.1016/j.copbio.2010.05.005.
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Zhang, Y. H. Percival. "Simpler Is Better: High-Yield and Potential Low-Cost Biofuels Production through Cell-Free Synthetic Pathway Biotransformation (SyPaB)." ACS Catalysis 1, no. 9 (July 27, 2011): 998–1009. http://dx.doi.org/10.1021/cs200218f.
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Wang, Lin, Chiam Yu Ng, Satyakam Dash, and Costas D. Maranas. "Exploring the combinatorial space of complete pathways to chemicals." Biochemical Society Transactions 46, no. 3 (April 6, 2018): 513–22. http://dx.doi.org/10.1042/bst20170272.
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Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors. The procedure then identifies the minimum number of intervening reactions to connect the source and sink metabolites. We also further the pathway design procedure by expanding the search space to include both known and hypothetical reactions, represented by reaction rules, in a new tool termed novoStoic. Reaction rules are derived based on a mixed-integer linear programming (MILP) compatible reaction operator, which allow us to explore natural promiscuous enzymes, engineer candidate enzymes that are not already promiscuous as well as design de novo enzymes. The identified biochemical reaction rules then guide novoStoic to design routes that expand the currently known biotransformation space using a single MILP modeling procedure. We demonstrate the use of the two computational tools in pathway elucidation by designing novel synthetic routes for isobutanol.
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Chen, Xuefei, Min Xu, Jin Lü, Jianguo Xu, Yemin Wang, Shuangjun Lin, Zixin Deng, and Meifeng Tao. "Biosynthesis of Tropolones inStreptomycesspp.: Interweaving Biosynthesis and Degradation of Phenylacetic Acid and Hydroxylations on the Tropone Ring." Applied and Environmental Microbiology 84, no. 12 (April 13, 2018): e00349-18. http://dx.doi.org/10.1128/aem.00349-18.
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ABSTRACTTropolonoids are important natural products that contain a unique seven-membered aromatic tropolone core and exhibit remarkable biological activities. 3,7-Dihydroxytropolone (DHT) isolated fromStreptomycesspecies is a multiply hydroxylated tropolone exhibiting antimicrobial, anticancer, and antiviral activities. In this study, we determined the DHT biosynthetic pathway by heterologous expression, gene deletion, and biotransformation. Ninetrlgenes and some of the aerobic phenylacetic acid degradation pathway genes (paa) located outside thetrlbiosynthetic gene cluster are required for the heterologous production of DHT. ThetrlAgene encodes a single-domain protein homologous to the C-terminal enoyl coenzyme A (enoyl-CoA) hydratase domain of PaaZ. TrlA truncates the phenylacetic acid catabolic pathway and redirects it toward the formation of heptacyclic intermediates. TrlB is a 3-deoxy-d-arabino-heptulosonic acid-7-phosphate (DAHP) synthase homolog. TrlH is an unusual bifunctional protein bearing an N-terminal prephenate dehydratase domain and a C-terminal chorismate mutase domain. TrlB and TrlH enhancedde novobiosynthesis of phenylpyruvate, thereby providing abundant precursor for the prolific production of DHT inStreptomycesspp. Six seven-membered carbocyclic compounds were identified from thetrlC,trlD,trlE, andtrlFdeletion mutants. Four of these chemicals, including 1,4,6-cycloheptatriene-1-carboxylic acid, tropone, tropolone, and 7-hydroxytropolone, were verified as key biosynthetic intermediates. TrlF is required for the conversion of 1,4,6-cycloheptatriene-1-carboxylic acid into tropone. The monooxygenases TrlE and TrlCD catalyze the regioselective hydroxylations of tropone to produce DHT. This study reveals a natural association of anabolism of chorismate and phenylpyruvate, catabolism of phenylacetic acid, and biosynthesis of tropolones inStreptomycesspp.IMPORTANCETropolonoids are promising drug lead compounds because of the versatile bioactivities attributed to their highly oxidized seven-membered aromatic ring scaffolds. Our present study provides clear insight into the biosynthesis of 3,7-dihydroxytropolone (DHT) through the identification of key genes responsible for the formation and modification of the seven-membered aromatic core. We also reveal the intrinsic mechanism of elevated production of DHT and related tropolonoids inStreptomycesspp. The study on DHT biosynthesis inStreptomycesexhibits a good example of antibiotic production in which both anabolic and catabolic pathways of primary metabolism are interwoven into the biosynthesis of secondary metabolites. Furthermore, our study sets the stage for metabolic engineering of the biosynthetic pathway for natural tropolonoid products and provides alternative synthetic biology tools for engineering novel tropolonoids.
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Saniewski, Marian, Marcin Horbowicz, and Sirichai Kanlayanarat. "The Biological Activities of Troponoids and Their Use in Agriculture A Review." Journal of Horticultural Research 22, no. 1 (September 10, 2014): 5–19. http://dx.doi.org/10.2478/johr-2014-0001.
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AbstractChemical compounds containing the tropone structure (2,4,6-cycloheptatrien-1-one), in their molecule, called troponoids, characterized by a seven-membered ring, are distributed in some plants, bacteria and fungi, although they are relatively rare. ß-Thujaplicin (2-hydroxy-4-isopropyl-2,4,6-cycloheptatrien-1-one), also known as hinokitiol, is a natural compound found in several plants of the Cupressaceae family. Besides hinokitiol, related compounds were identified in Cupressaceae trees. It has been demonstrated that hinokitiol and its derivatives have various biological effects, such as antibacterial, antifungal, insecticidal, antimalarial, antitumor, anti-ischemic, iron chelating and the inhibitory activity against polyphenol oxidase activity. Activity similar to ß-thujaplicin has tropolone and its derivatives, which are not present nature. Due to the high scientific and practical interest, synthetic ß-thujaplicin and other troponoids have been produced for many years. In this review, the major biological effects of troponoids, mostly ß-thujaplicin and tropolone, on tyrosinase and polyphenol oxidase activity, ethylene production, antibacterial, antifungal and insecticidal activities, and biotransformation of ß-thujaplicin by cultured plant cells are presented. Accumulation of ß-thujaplicin and related troponoids has been shown in cell cultures of Cupressus lusitanica and other species of Cupressaceae. The biosynthetic pathway of the troponoids in plants, bacteria and fungi has been also briefly described.
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Gupta, Mukta, and Vasu Nair. "Adenosine Deaminase in Nucleoside Synthesis. A Review." Collection of Czechoslovak Chemical Communications 71, no. 6 (2006): 769–87. http://dx.doi.org/10.1135/cccc20060769.
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Adenosine deaminase (ADA) is an enzyme in the purine salvage pathway that catalyzes the deamination of adenosine and deoxyadenosine to inosine and deoxyinosine, respectively. This deamination is an important factor in limiting the usefulness of adenosine analogues in chemotherapy. However, the biocatalysis by ADA is also a useful transformation in enzymatic synthesis. In this review, examples from both the principal investigator's laboratory and from the literature, which depict the synthetic usefulness of this enzyme in deamination, dehalogenation, demethoxylation reactions and in diastereoisomeric resolution, are presented. It is not the intent of this review to comprehensively list all of the biotransformations induced by adenosine deaminase, but rather to present representative examples to highlight the powerful synthetic utility of this enzyme. A review with 72 references.
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Moore, Simon J. "Enzyme alchemy: cell-free synthetic biochemistry for natural products." Emerging Topics in Life Sciences 3, no. 5 (September 4, 2019): 529–35. http://dx.doi.org/10.1042/etls20190083.
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Cell-free synthetic biochemistry aims to engineer chemical biology by exploiting biosynthetic dexterity outside of the constraints of a living cell. One particular use is for making natural products, where cell-free systems have initially demonstrated feasibility in the biosynthesis of a range of complex natural products classes. This has shown key advantages over total synthesis, such as increased yield, enhanced regioselectivity, use of reduced temperatures and less reaction steps. Uniquely, cell-free synthetic biochemistry represents a new area that seeks to advance upon these efforts and is particularly useful for defining novel synthetic pathways to replace natural routes and optimising the production of complex natural product targets from low-cost precursors. Key challenges and opportunities will include finding solutions to scaled-up cell-free biosynthesis, as well as the targeting of high value and toxic natural products that remain challenging to make either through whole-cell biotransformation platforms or total synthesis routes. Although underexplored, cell-free synthetic biochemistry could also be used to develop ‘non-natural’ natural products or so-called xenobiotics for novel antibiotics and drugs, which can be difficult to engineer directly within a living cell.
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Arora, Pankaj Kumar, Kartik Dhar, Rafael Alejandro Veloz García, and Ashutosh Sharma. "Biotransformation of Indole to 3-Methylindole byLysinibacillus xylanilyticusStrain MA." Journal of Chemistry 2015 (2015): 1–5. http://dx.doi.org/10.1155/2015/425329.
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An indole-biotransforming strain MA was identified asLysinibacillus xylanilyticuson the basis of the 16S rRNA gene sequencing. It transforms indole completely from the broth culture in the presence of an additional carbon source (i.e., sodium succinate). Gas-chromatography-mass spectrometry identified indole-3-acetamide, indole-3-acetic acid, and 3-methylindole as transformation products. Tryptophan-2-monooxygenase activity was detected in the crude extracts of indole-induced cells of strain MA, which confirms the formation of indole-3-acetamide from tryptophan in the degradation pathway of indole. On the basis of identified metabolites and enzyme assay, we have proposed a new transformation pathway for indole degradation. Indole was first transformed to indole-3-acetamide via tryptophan. Indole-3-acetamide was then transformed to indole-3-acetic acid that was decarboxylated to 3-methylindole. This is the first report of a 3-methylindole synthesis via the degradation pathway of indole.
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Lou, Hanghang, Hao Li, Shengliang Zhang, Hongyun Lu, and Qihe Chen. "A Review on Preparation of Betulinic Acid and Its Biological Activities." Molecules 26, no. 18 (September 14, 2021): 5583. http://dx.doi.org/10.3390/molecules26185583.
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Betulinic acid, a pentacyclic triterpene, is distributed in a variety of plants, such as birch, eucalyptus and plane trees. It shows a wide spectrum of biological and pharmacological properties, such as anti-inflammatory, antibacterial, antiviral, antidiabetic, antimalarial, anti-HIV and antitumor effects. Among them, the antitumor activity of betulinic acid has been extensively studied. However, obtaining betulinic acid from natural resources can no longer meet the needs of medicine and nutrition, so methods such as chemical synthesis and microbial biotransformation have also been used to prepare betulinic acid. At the same time, with the development of synthetic biology and genetic engineering, and the elucidation of the biosynthetic pathways of terpenoid, the biosynthesis of betulinic acid has also been extensively researched. This article reviews the preparation of betulinic acid and its pharmacological activities, in order to provide a reference for the research and utilization of betulinic acid.
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Koko, Marwa Y. F., Rokayya Sami, Bertrand Muhoza, Ebtihal Khojah, and Ahmed M. A. Mansour. "Promising Pathway of Thermostable Mannitol Dehydrogenase (MtDH) from Caldicellulosiruptor hydrothermalis 108 for D-Mannitol Synthesis." Separations 8, no. 6 (June 1, 2021): 76. http://dx.doi.org/10.3390/separations8060076.
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In this study, we conducted the characterization and purification of the thermostable mannitol dehydrogenase (MtDH) from Caldicellulosiruptor hydrothermalis 108. Furthermore, a coupling-enzyme system was designed using (MtDH) from Caldicellulosiruptor hydrothermalis 108 and formate dehydrogenase (FDH) from Ogataea parapolymorpha. The biotransformation system was constructed using Escherichia coli whole cells. The purified enzyme native and subunit molecular masses were 76.7 and 38 kDa, respectively, demonstrating that the enzyme was a dimer. The purified and couple enzyme system results were as follows; the optimum pH for the reduction and the oxidation was 7.0 and 8.0, the optimum temperature was 60 °C, the enzyme activity was inhibited by EDTA and restored by zinc. Additionally, no activity was detected with NADPH and NADP. The purified enzyme showed high catalytic efficiency Kcat 385 s−1, Km 31.8 mM, and kcat/Km 12.1 mM−1 s−1 for D-fructose reduction. Moreover, the purified enzyme retained 80%, 75%, 60%, and 10% of its initial activity after 4 h at 55, 60, 65, and 75 °C, respectively. D-mannitol yield was achieved via HPLC. Escherichia coli are the efficient biotransformation mediator to produce D-mannitol (byproducts free) at high temperature and staple pH, resulting in a significant D-mannitol conversation (41 mg/mL) from 5% D-fructose.
Dissertations / Theses on the topic "Synthetic pathway biotransformation"
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Zhu, Zhiguang. "Enzymatic fuel cells via synthetic pathway biotransformation." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/51948.
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Enzyme-catalyzed biofuel cells would be a great alternative to current battery technology, as they are clean, safe, and capable of using diverse and abundant renewable biomass with high energy densities, at mild reaction conditions. However, currently, three largest technical challenges for emerging enzymatic fuel cell technologies are incomplete oxidation of most fuels, limited power output, and short lifetime of the cell.
Synthetic pathway biotransformation is a technology of assembling a number of enzymes coenzymes for producing low-value biocommodities. In this work, it was applied to generate bioelectricity for the first time. Non-natural enzymatic pathways were developed to utilize maltodextrin and glucose in enzymatic fuel cells. Three immobilization approaches were compared for preparing enzyme electrodes. Thermostable enzymes from thermophiles were cloned and expressed for improving the lifetime and stability of the cell. To further increase the power output, non-immobilized enzyme system was demonstrated to have higher power densities compared to those using immobilized enzyme system, due to better mass transfer and retained native enzyme activities.
With the progress on pathway development and power density/stability improvement in enzymatic fuel cells, a high energy density sugar-powered enzymatic fuel cell was demonstrated. The enzymatic pathway consisting of 13 thermostable enzymes enabled the complete oxidation of glucose units in maltodextrin to generate 24 electrons, suggesting a high energy density of such enzymatic fuel cell (300 Wh/kg), which was several folds higher than that of a lithium-ion battery. Maximum power density was 0.74 mW/cm2 at 50 deg C and 20 mM fuel concentration, which was sufficient to power a digital clock or a LED light.
These results suggest that enzymatic fuel cells via synthetic pathway biotransformation could achieve high energy density, high power density and increased lifetime. Future efforts should be focused on further increasing power density and enzyme stability in order to make enzymatic fuel cells commercially applicable.Ph. D.
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Sun, Fangfang. "Development of Building Blocks - Thermostable Enzymes for Synthetic Pathway Biotransformation (SyPaB)." Thesis, Virginia Tech, 2012. http://hdl.handle.net/10919/77009.
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Hydrogen production from abundant renewable biomass would decrease reliance on crude oils, achieve nearly zero net greenhouse gas emissions, create more jobs, and enhance national energy security. Cell-free synthetic pathway biotransformation (SyPaB) is the implementation of complicated chemical reaction by the in vitro assembly of numerous enzymes and coenzymes that microbes cannot do. One of the largest challenges is the high cost and instability of enzymes and cofactors. To overcome this obstacle, strong motivations have driven intensive efforts in discovering, engineering, and producing thermostable enzymes.
In this project, ribose-5-phosphate isomerase (RpiB), one of the most important enzymes in the pentose phosphate pathway, was cloned from a thermophile Thermotoga maritima, and heterologously expressed in Escherichia coli, purified and characterized. High-purity RpiB was obtained by heat pretreatment through its optimization in buffer choice, buffer pH, as well as temperature and duration of pretreatment. This enzyme had the maximum activity at 80°C and pH 6.5-8.0. It had a half lifetime of 71 h at 60°C, resulting in its turn-over number of more than 2 x108 mol of product per mol of enzyme. Another two thermostable enzymes glucose-6-phosphate dehydrogenase (G6PDH) and diaphorase (DI) and their fusion proteins G6PDH-DI and DI-G6PDH were cloned from Geobacillus stearothermophilus, heterologouely expressed in E. coli and purified through its His-tag. The individual proteins G6PDH and DI have good thermostability and reactivity. However, the presence of DI in fusion proteins drastically decreased G6DPH activity. However, a mixture of G6PDH and a fusion protein G6PDH-DI not only restored G6PDH activity through the formation of heteromultimeric network but also facilitated substrate channeling between DI and G6PDH, especially at low enzyme concentrations.
My researches would provide important building blocks for the on-going projects: high-yield hydrogen production through cell-free enzymatic pathways and electrical energy production through enzymatic fuel cells.Master of Science
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Ye, Xinhao. "Enzymatic Production of Cellulosic Hydrogen by Cell-free Synthetic Pathway Biotransformation(SyPaB)." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/77141.
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The goals of this research were 1) to produce hydrogen in high yields from cellulosic materials and water by synthetic pathway biotranformation (SyPaB), and 2) to increase the hydrogen production rate to a level comparable to microbe-based methods (~ 5 mmol H2/L/h).
Cell-free SyPaB is a new biocatalysis technology that integrates a number of enzymatic reactions from four different metabolic pathways, e.g. glucan phosphorylation, pentose phosphate pathway, gluconeogenesis, and hydrogenase-catalyzed hydrogen production, so as to release 12 mol hydrogen per mol glucose equivalent. To ensure the artificial enzymatic pathway would work for hydrogen production, thermodynamic analysis was firstly conducted, suggesting that the artificial enzymatic pathway would spontaneously release hydrogen from cellulosic materials. A kinetic model was constructed to assess the rate-limited step(s) through metabolic control analysis. Three phosphorylases, i.e. α-glucan phosphorylase, cellobiose phosphorylase, and cellodextrin phosphorylase, were cloned from a thermophile Clostridium thermocellum, and heterologously expressed in Escherichia coli, purified and characterized in detail. Finally, up to 93% of hydrogen was produced from cellulosic materials (11.2 mol H2/mol glucose equivalent). A nearly 20-fold enhancement in hydrogen production rates has been achieved by increasing the rate-limiting hydrogenase concentration, increasing the substrate loading, and elevating the reaction temperature slightly from 30 to 32°C. The hydrogen production rates were higher than those of photobiological systems and comparable to the rates reported in dark fermentations.
Now the hydrogen production is limited by the low stabilities and low activities of various phosphorylases. Therefore, non-biologically based methods have been applied to prolong the stability of α-glucan phosphorylases. The catalytic potential of cellodextrin phosphorylase has been improved to degrade insoluble cellulose by fusion of a carbohydrate-binding module (CBM) family 9 from Thermotoga maritima Xyn10A. The inactivation halftime of C. thermocellum cellobiose phosphorylase has been enhanced by three-fold at 70°C via a combination of rational design and directed evolution. The phosphorylases with improved properties would work as building blocks for SyPaB and enabled large-scale enzymatic production of cellulosic hydrogen.Ph. D.
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Liao, Hehuan. "High-Yield Cellulosic Hydrogen Production by Cell-Free Synthetic Cascade Enzymes: Minimal Bacterial Cellulase Cocktail and Thermostable Polyphosphate Glucokinase." Thesis, Virginia Tech, 2011. http://hdl.handle.net/10919/76997.
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Hydrogen production from abundant renewable biomass would decrease reliance on crude oils, achieve nearly zero net greenhouse gas emissions, create more jobs, and enhance national energy security. Cell-free synthetic pathway biotransformation (SyPaB) is the implementation of complicated chemical reaction by the in vitro assembly of numerous enzymes and coenzymes. Two of the biggest challenges for its commercialization are: effective release of fermentable sugars from pretreated biomass, and preparations of thermostable enzymes with low-cost.
The hydrolysis performance of 21 reconstituted bacterial cellulase mixtures containing the glycoside hydrolase family 5 Bacillus subtilis endoglucanase, family 9 Clostridium phytofermentans processive endoglucanase, and family 48 Clostridium phytofermentans cellobiohydrolase was investigated on microcrystalline cellulose (Avicel) and regenerated amorphous cellulose (RAC). The optimal ratios for maximum cellulose digestibility were dynamic for Avicel but nearly fixed for RAC. Processive endoglucanase CpCel9 was most important for high cellulose digestibility regardless of substrate type. These results suggested that the hydrolysis performance of reconstituted cellulase cocktail strongly depended on experimental conditions.
Thermobifida fusca YX was hypothesized to have a thermophilic polyphosphate glucokinase. T. fusca YX ORF Tfu_1811 encoding a putative PPGK was cloned and the recombinant protein fused with a family 3 cellulose-binding module (CBM-PPGK) was over expressed in Escherichia coli. By a simple one-step immobilization, the half-life time increased to 2 h, at 50 °C. These results suggest that this enzyme was the most thermostable PPGK reported.
My studies would provide important information for the on-going project: high-yield hydrogen production from cellulose by cell-free synthetic enzymatic pathway.Master of Science
Book chapters on the topic "Synthetic pathway biotransformation"
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Jahangeer, Muhammad, Areej Riasat, Zahed Mahmood, Muhammad Numan, Naveed Munir, Mehvish Ashiq, Muhammad Asad, Usman Ali, and Mahwish Salman. "Secondary Metabolites from Saccharomyces cerevisiae Species with Anticancer Potential." In Saccharomyces. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.95067.
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Chemotherapeutic agents produce from numerous sources such as animals, plants and micro-organisms are derived from the natural products. Although the existing therapeutic pipeline lacks fungal-derived metabolites, but hundreds of secondary metabolites derived from fungi are known to be possible chemotherapies. Over the past three decades, several secondary metabolites such as flavonoids, alkaloids, phenolic and polyketides have been developed by Saccharomyces cerevisiae species with exciting activities that considered valued for the growth of new chemotherapeutic agents. Many secondary metabolites are protective compounds which prevent abiotic and biotic stresses, i.e. predation, infection, drought and ultraviolet. Though not taking part in a living cell’s central metabolism, secondary metabolites play an important role in the function of an organism. Nevertheless, due to slow biomass build-up and inadequate synthesis by the natural host the yield of secondary metabolites is low by direct isolation. A detailed comprehension of biosynthetic pathways for development of secondary metabolites are necessary for S. cerevisiae biotransformation. These metabolites have higher inhibitory effect, specificity among cancer and normal cells, and the mechanism of non-apoptotic cell killing. This study shows the significance of bioactive compounds produced by S. cerevisiae species with their possible activity and value in chemotherapeutic drugs pipeline. The isolation and alteration of these natural secondary metabolites would promote the development of chemotherapeutic drugs.