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Lv Y, Chang J, Zhang W, Dong H, Chen S, Wang X, Zhao A, Zhang S, Alam MA, Wang S, Du C, Xu J, Wang W, Xu P. Improving Microbial Cell Factory Performance by Engineering SAM Availability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3846-3871. [PMID: 38372640 DOI: 10.1021/acs.jafc.3c09561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Methylated natural products are widely spread in nature. S-Adenosyl-l-methionine (SAM) is the secondary abundant cofactor and the primary methyl donor, which confer natural products with structural and functional diversification. The increasing demand for SAM-dependent natural products (SdNPs) has motivated the development of microbial cell factories (MCFs) for sustainable and efficient SdNP production. Insufficient and unsustainable SAM availability hinders the improvement of SdNP MCF performance. From the perspective of developing MCF, this review summarized recent understanding of de novo SAM biosynthesis and its regulatory mechanism. SAM is just the methyl mediator but not the original methyl source. Effective and sustainable methyl source supply is critical for efficient SdNP production. We compared and discussed the innate and relatively less explored alternative methyl sources and identified the one involving cheap one-carbon compound as more promising. The SAM biosynthesis is synergistically regulated on multilevels and is tightly connected with ATP and NAD(P)H pools. We also covered the recent advancement of metabolic engineering in improving intracellular SAM availability and SdNP production. Dynamic regulation is a promising strategy to achieve accurate and dynamic fine-tuning of intracellular SAM pool size. Finally, we discussed the design and engineering constraints underlying construction of SAM-responsive genetic circuits and envisioned their future applications in developing SdNP MCFs.
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Affiliation(s)
- Yongkun Lv
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Jinmian Chang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weiping Zhang
- Bloomage Biotechnology Corporation Limited, 678 Tianchen Street, Jinan, Shandong 250101, China
| | - Hanyu Dong
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Song Chen
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Xian Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Anqi Zhao
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, China
| | - Shen Zhang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Md Asraful Alam
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Chaojun Du
- Nanyang Research Institute of Zhengzhou University, Nanyang Institute of Technology, No. 80 Changjiang Road, Nanyang 473004, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
- National Key Laboratory of Biobased Transportation Fuel Technology, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Palo Alto, California 94305, United States
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China
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2
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Fischer A, Sellner M, Neranjan S, Smieško M, Lill MA. Potential Inhibitors for Novel Coronavirus Protease Identified by Virtual Screening of 606 Million Compounds. Int J Mol Sci 2020; 21:E3626. [PMID: 32455534 PMCID: PMC7279339 DOI: 10.3390/ijms21103626] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023] Open
Abstract
The rapid outbreak of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China followed by its spread around the world poses a serious global concern for public health. To this date, no specific drugs or vaccines are available to treat SARS-CoV-2 despite its close relation to the SARS-CoV virus that caused a similar epidemic in 2003. Thus, there remains an urgent need for the identification and development of specific antiviral therapeutics against SARS-CoV-2. To conquer viral infections, the inhibition of proteases essential for proteolytic processing of viral polyproteins is a conventional therapeutic strategy. In order to find novel inhibitors, we computationally screened a compound library of over 606 million compounds for binding at the recently solved crystal structure of the main protease (Mpro) of SARS-CoV-2. A screening of such a vast chemical space for SARS-CoV-2 Mpro inhibitors has not been reported before. After shape screening, two docking protocols were applied followed by the determination of molecular descriptors relevant for pharmacokinetics to narrow down the number of initial hits. Next, molecular dynamics simulations were conducted to validate the stability of docked binding modes and comprehensively quantify ligand binding energies. After evaluation of potential off-target binding, we report a list of 12 purchasable compounds, with binding affinity to the target protease that is predicted to be more favorable than that of the cocrystallized peptidomimetic compound. In order to quickly advise ongoing therapeutic intervention for patients, we evaluated approved antiviral drugs and other protease inhibitors to provide a list of nine compounds for drug repurposing. Furthermore, we identified the natural compounds (-)-taxifolin and rhamnetin as potential inhibitors of Mpro. Rhamnetin is already commercially available in pharmacies.
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Affiliation(s)
| | | | | | - Martin Smieško
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.); (S.N.)
| | - Markus A. Lill
- Computational Pharmacy, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (A.F.); (M.S.); (S.N.)
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Magar RT, Sohng JK. A Review on Structure, Modifications and Structure-Activity Relation of Quercetin and Its Derivatives. J Microbiol Biotechnol 2020; 30:11-20. [PMID: 31752056 PMCID: PMC9728256 DOI: 10.4014/jmb.1907.07003] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Quercetin and its derivatives are important metabolites that belong to the flavonol class of flavonoids. Quercetin and some of the conjugates have been approved by the FDA for human use. They are widely distributed among plants and have various biological activities, such as being anticancer, antiviral, and antioxidant. Hence, the biosynthesis of novel derivatives is an important field of research. Glycosylation and methylation are two important modification strategies that have long been used and have resulted in many novel metabolites that are not present in natural sources. A strategy for modifying quercetin in E. coli by means of glycosylation, for example, involves overexpressing respective glycosyltransferases (GTs) in the host and metabolic engineering for increasing nucleoside diphosphate sugar (NDP sugar). Still others have used microorganisms other than E. coli, such as Streptomyces sp., for the biotransformation process. The overall study of the structural activity relationship has revealed that modification of some residues in quercetin decreased one activity but increased others. This review summarizes all of the information mentioned above.
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Affiliation(s)
- Rubin Thapa Magar
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan 3460, Republic of Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, SunMoon University, Asan 3460, Republic of Korea,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea,Corresponding author Phone: +82-41-530-2246 Fax: +82-41-530-8229 E-mail:
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Assirey E, Alsaggaf A, Naqvi A, Moussa Z, Okasha RM, Afifi TH, Abd-El-Aziz AS. Synthesis, Biological Assessment, and Structure Activity Relationship Studies of New Flavanones Embodying Chromene Moieties. Molecules 2020; 25:molecules25030544. [PMID: 32012737 PMCID: PMC7037824 DOI: 10.3390/molecules25030544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/15/2020] [Accepted: 01/26/2020] [Indexed: 02/04/2023] Open
Abstract
Novel flavanones that incorporate chromene motifs are synthesized via a one-step multicomponent reaction. The structures of the new chromenes are elucidated by using IR, 1H-NMR, 13C-NMR, 1H-1H COSY, HSQC, HMBC, and elemental analysis. The new compounds are screened for their in vitro antimicrobial and cytotoxic activities. The antimicrobial properties are investigated and established against seven human pathogens, employing the agar well diffusion method and the minimum inhibitory concentrations. A majority of the assessed derivatives are found to exhibit significant antimicrobial activities against most bacterial strains, in comparison to standard reference drugs. Moreover, their cytotoxicity is appraised against four different human carcinoma cell lines: human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), human breast adenocarcinoma (MCF-7), and adenocarcinoma human alveolar basal epithelial cell (A-549). All the desired compounds are subjected to in-silico studies, forecasting their drug likeness, bioactivity, and the absorption, distribution, metabolism, and excretion (ADME) properties prior to their synthetic assembly. The in-silico molecular docking evaluation of all the targeted derivatives is undertaken on gyrase B and the cyclin-dependent kinase. The in-silico predicted outcomes were endorsed by the in vitro studies.
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Affiliation(s)
- Eman Assirey
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
| | - Azhaar Alsaggaf
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
| | - Arshi Naqvi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain 15551, UAE;
| | - Rawda M. Okasha
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
| | - Tarek H. Afifi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (E.A.); (A.A.); (A.N.); (R.M.O.)
| | - Alaa S. Abd-El-Aziz
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
- Correspondence: ; Tel.: +1-(902)-566-0400
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Tiwari P, Mishra KP. Flavonoids sensitize tumor cells to radiation: molecular mechanisms and relevance to cancer radiotherapy. Int J Radiat Biol 2019; 96:360-369. [PMID: 31738629 DOI: 10.1080/09553002.2020.1694193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Purpose: Radiobiological research continues to focus on finding newer strategies for enhanced killing of tumor cells by ionizing radiation. In recent years, chemotherapeutic drugs have been found to possess the capabilities to sensitize tumor cells without affecting the normal cells. There have been increasing research efforts to identify novel and nontoxic compounds which cause minimal or no harm to normal cells but maximize tumor toxicity response to radiation exposure. Extensive researches on flavonoids that are compounds derived from plants have shown that these have promising abilities as radioprotectors and radiosensitizers.Conclusions: In this review, we examine the role of flavonoids as potential radiosensitizers, review the underlying molecular mechanisms and discuss their potential usefulness in improving cancer radiotherapy. It is emphasized that obtaining a deeper insight into the molecular mechanisms underlying the combined action of flavonoids and ionizing radiation may provide new directions for radiobiological research applicable to the much needed enhanced selective tumor cytotoxicity to treatment agents.
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Affiliation(s)
- Prabha Tiwari
- National Institutes of Biomedical Innovation Health and Nutrition, Ibaraki, Osaka, Japan
| | - Kaushala Prasad Mishra
- Foundation for Education and Research, Ex Bhabha Atomic Research Center, Mumbai, Maharashtra, India
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Abstract
Flavonoids are tricyclic polyphenolic compounds naturally occurring in plants. Being nature’s antioxidants flavonoids have been shown to reduce the damages induced by oxidative stress in cells. Besides being an antioxidant, flavonols are demonstrated to have anti-infective properties, i.e., antiviral, antifungal, anti-angiogenic, anti-tumorigenic, and immunomodulatory bioproperties. Plants use them as one of their defense mechanisms against radiation-induced DNA damage and also for fungal infections. The use of flavonols for fabrication of new drugs has been underway with objectives to develop safer and effective therapeutic agents. This review covers 15 flavonols for their structure, biological properties, role in plant metabolisms, and current research focused on computational drug design using flavonols for searching drug leads.
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7
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Koirala N, Pandey RP, Thuan NH, Ghimire GP, Jung HJ, Oh TJ, Sohng JK. Metabolic engineering of Escherichia coli for the production of isoflavonoid-4'-O-methoxides and their biological activities. Biotechnol Appl Biochem 2017; 66:484-493. [PMID: 26498482 DOI: 10.1002/bab.1452] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/16/2015] [Indexed: 12/20/2022]
Abstract
Isoflavonoid representatives such as genistein and daidzein are highly potent anticancer, antibacterial, and antioxidant agents. It have been demonstrated that methylation of flavonoids enhanced the transporting ability, which lead to facilitated absorption and greatly increased bioavailability. In this paper, genetically engineered Escherichia coli was reconstructed by harboring E. coli K12-derived metK encoding S-adenosine-l-methionine (SAM) synthase (accession number: K02129) for enhancement of SAM as a precursor and Streptomyces avermitilis originated SaOMT2 (O-methyltransferase, accession number: NP_823558) for methylation of daidzein and genistein as preferred substrates. The formation of desired products via biotransformation including 4'-O-methyl-genistein and 4'-O-methyl-daidzein was confirmed individually by using chromatographical methods such as high-performance liquid chromatography, liquid chromatography/time-of-flight/mass spectrometry (LC-TOF-MS), and nuclear magnetic resonance (NMR), and NMR (1 H and 13 C). Furthermore, substrates concentration, incubation time, and media parameters were optimized using flask culture. Finally, the most fit conditions were applied for fed-batch fermentation with scale-up to 3 L (working volume) to obtain the maximum yield of the products including 164.25 µM (46.81 mg/L) and 382.50 µM (102.88 mg/L) for 4'-O-methyl genistein and 4'-O-methyl daidzein, respectively. In particular, potent inhibitory activities of those isoflavonoid methoxides against the growth of cancer line (B16F10, AGS, and HepG2) and human umbilical vein endothelial cells were investigated and demonstrated. Taken together, this research work described the production of isoflavonoid-4'-O-methoxides by E. coli engineering, improvement of production, characterization of produced compounds, and preliminary in vitro biological activities of the flavonoids being manufactured.
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Affiliation(s)
- Niranjan Koirala
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea
| | - Ramesh Prasad Pandey
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea.,Department of Life Science and Biochemical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea
| | - Nguyen Huy Thuan
- Center for Molecular Biology, Institute of Research and Development, Duy Tan University, Danang city, Vietnam
| | - Gopal Prasad Ghimire
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea
| | - Hye Jin Jung
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea.,Department of Life Science and Biochemical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea
| | - Tae-Jin Oh
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea.,Department of Life Science and Biochemical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea
| | - Jae Kyung Sohng
- Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea.,Department of Life Science and Biochemical Engineering, Sun Moon University, Asansi, Chungnam, Republic of Korea
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8
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Koirala N, Thuan NH, Ghimire GP, Thang DV, Sohng JK. Methylation of flavonoids: Chemical structures, bioactivities, progress and perspectives for biotechnological production. Enzyme Microb Technol 2016; 86:103-16. [PMID: 26992799 DOI: 10.1016/j.enzmictec.2016.02.003] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/02/2016] [Accepted: 02/09/2016] [Indexed: 12/16/2022]
Abstract
Among the natural products, flavonoids have been particularly attractive, highly studied and become one of the most important promising agent to treat cancer, oxidant stress, pathogenic bacteria, inflammations, cardio-vascular dysfunctions, etc. Despite many promising roles of flavonoids, expectations have not been fulfilled when studies were extended to the in vivo condition, particularly in humans. Instability and very low oral bioavailability of dietary flavonoids are the reasons behind this. Researches have demonstrated that the methylation of these flavonoids could increase their promise as pharmaceutical agents leading to novel applications. Methylation of the flavonoids via theirs free hydroxyl groups or C atom dramatically increases their metabolic stability and enhances the membrane transport, leading to facilitated absorption and highly increased oral bioavailability. In this paper, we concentrated on analysis of flavonoid methoxides including O- and C-methoxide derivatives in aspect of structure, bioactivities and description of almost all up-to-date O- and C-methyltransferases' enzymatic characteristics. Furthermore, modern biological approaches for synthesis and production of flavonoid methoxides using metabolic engineering and synthetic biology have been focused and updated up to 2015. This review will give a handful information regarding the methylation of flavonoids, methyltransferases and biotechnological synthesis of the same.
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Affiliation(s)
- Niranjan Koirala
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 100, Kalsan-ri, Tangjeonmyun, Asansi, Chungnam 336-708, Republic of Korea.
| | - Nguyen Huy Thuan
- Center for Molecular Biology, Institute of Research and Development, Duy Tan University, K7/25 Quang Trung Street, Haichau District, Danang City, Viet Nam.
| | - Gopal Prasad Ghimire
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 100, Kalsan-ri, Tangjeonmyun, Asansi, Chungnam 336-708, Republic of Korea.
| | - Duong Van Thang
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 100, Kalsan-ri, Tangjeonmyun, Asansi, Chungnam 336-708, Republic of Korea.
| | - Jae Kyung Sohng
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 100, Kalsan-ri, Tangjeonmyun, Asansi, Chungnam 336-708, Republic of Korea.
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Abstract
The term superfood refers to food with high levels of either nutrient or bioactive phytochemicals with human health benefits. Phytochemicals are naturally occurring compounds in plants that provide their color, flavor and odor. Phenolic compounds form the major constituents of phytochemicals. Plant traits in phytochemical production are tightly bound with the genome while modified markedly by the environmental conditions. Here, we studied the effect of supplemented blue light on the production of several phenolics in the leaves of tomato, basil and parsley, which are widely cultivated food plant species. The results indicated doubled or higher increases in the accumulation of several species-specific phenolic acids or flavonoids. In conclusion, we showed for the first time, that supplemented blue light results in high yield improvement of phytochemicals related to superfood products.
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Affiliation(s)
- Kari Taulavuori
- Department of Biology, University of Oulu, P. O. Box 3000, FIN-90014 University of Oulu, Finland
| | - Riitta Julkunen-Tiitto
- Department of Biology, University of Eastern Finland, P.O. Box 111, FIN-80101, Joensuu, Finland
| | - Valtteri Hyöky
- Department of Biology, University of Oulu, P. O. Box 3000, FIN-90014 University of Oulu, Finland
| | - Erja Taulavuori
- Department of Biology, University of Oulu, P. O. Box 3000, FIN-90014 University of Oulu, Finland
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Shin SY, Yoon H, Ahn S, Kim DW, Kim SH, Koh D, Lee YH, Lim Y. Chromenylchalcones showing cytotoxicity on human colon cancer cell lines and in silico docking with aurora kinases. Bioorg Med Chem 2013; 21:4250-8. [PMID: 23719279 DOI: 10.1016/j.bmc.2013.04.086] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 11/17/2022]
Abstract
Due to toxicity problems, various plant-derived compounds have been screened to find the chemotherapeutic agents. As anticancer therapeutic agents, chalcones have advantages such as poor interaction with DNA and low risk of mutagenesity. Chromenones show anticancer activities too. Therefore, hybrids of chalcone and chromenone may be potent chemotherapeutic agents. We prepared 16 synthetic chromenylchalcones and applied a clonogenic long-term survival assay method for them on HCT116 human colorectal cancer cell lines. One of chromenylchalcones tested here, chromenylchalcone 11, showed IC50 of 93.1nM which can be competed with the IC50 values of well-known flavonoids such as catechin gallate and epicatechin gallate. Further biological experiments including cell cycle analysis, apoptosis assay, Western blot analysis, and immunofluorescent microscopy were carried out for this compound. In addition, in vitro kinases binding assay performed to explain its molecular mechanism demonstrated the compound inhibited aurora kinases. The binding modes between chromenylchalcone 11 and aurora kinases were elucidated using in silico docking experiments. These findings could be used for designing cancer therapeutic or preventive plant-derived chromenylchalcone agents.
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Affiliation(s)
- Soon Young Shin
- Department of Biological Sciences, College of Biological Science and Biotechnology, Konkuk University, Seoul 143-701, South Korea
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11
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Pirie CM, De Mey M, Prather KLJ, Ajikumar PK. Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis. ACS Chem Biol 2013; 8:662-72. [PMID: 23373985 DOI: 10.1021/cb300634b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.
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Affiliation(s)
- Christopher M. Pirie
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
| | - Marjan De Mey
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
- Centre of
Expertise−Industrial Biotechnology and Biocatalysis, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Kristala L. Jones Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Parayil Kumaran Ajikumar
- Manus Biosynthesis Inc., Suite 102, 790 Memorial Drive, Cambridge, Massachusetts 02139,
United States
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12
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Design, synthesis and inhibitory activities of naringenin derivatives on human colon cancer cells. Bioorg Med Chem Lett 2012. [PMID: 23177257 DOI: 10.1016/j.bmcl.2012.10.130] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Based on the previous result, several naringenin derivatives modified at position 7 with bulky substituents were designed and synthesized, and their inhibitory effects on HCT116 human colon cancer cells were tested using a clonogenic assay. The half maximal inhibitory concentrations (IC(50)) of five naringenin derivatives ranged between 1.20 μM and 20.01 μM which are much better than naringenin used as a control. In addition, new structural modification at C-4 of flavanone results in improving both the anti-cancer effect and anti-oxidative effect. In vitro cyclin dependent kinase 2 (CDK2) binding assay was carried out based on the previous results. To elucidate the possible interaction between naringenin derivatives and CDK2, in silico docking study was performed. This result demonstrates the rationale for the different inhibitory activities of the naringenin derivatives. These findings could be used for designing cancer therapeutic or preventive flavanone-derived agents.
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13
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Liscombe DK, Louie GV, Noel JP. Architectures, mechanisms and molecular evolution of natural product methyltransferases. Nat Prod Rep 2012; 29:1238-50. [PMID: 22850796 DOI: 10.1039/c2np20029e] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The addition of a methyl moiety to a small chemical is a common transformation in the biosynthesis of natural products across all three domains of life. These methylation reactions are most often catalysed by S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTs). MTs are categorized based on the electron-rich, methyl accepting atom, usually O, N, C, or S. SAM-dependent natural product MTs (NPMTs) are responsible for the modification of a wide array of structurally distinct substrates, including signalling and host defense compounds, pigments, prosthetic groups, cofactors, cell membrane and cell wall components, and xenobiotics. Most notably, methylation modulates the bioavailability, bioactivity, and reactivity of acceptor molecules, and thus exerts a central role on the functional output of many metabolic pathways. Our current understanding of the structural enzymology of NPMTs groups these phylogenetically diverse enzymes into two MT-superfamily fold classes (class I and class III). Structural biology has also shed light on the catalytic mechanisms and molecular bases for substrate specificity for over fifty NPMTs. These biophysical-based approaches have contributed to our understanding of NPMT evolution, demonstrating how a widespread protein fold evolved to accommodate chemically diverse methyl acceptors and to catalyse disparate mechanisms suited to the physiochemical properties of the target substrates. This evolutionary diversity suggests that NPMTs may serve as starting points for generating new biocatalysts.
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Affiliation(s)
- David K Liscombe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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