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Zhu M, Qu J, Deng Q. Identification of potential inhibitors against Staphylococcus aureus shikimate dehydrogenase through virtual screening and susceptibility test. J Enzyme Inhib Med Chem 2024; 39:2301768. [PMID: 38234148 PMCID: PMC10798293 DOI: 10.1080/14756366.2024.2301768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024] Open
Abstract
Staphylococcus aureus shikimate dehydrogenase (SaSDH) plays a crucial role in the growth of Staphylococcus aureus (S. aureus), but absent in mammals and therefore a potential target for antibacterial drugs to treat drug-resistant S. aureus infection. In this study, a 3D model of SaSDH was constructed by homology modelling and inhibitors of SaSDH were screened through virtual screening. (-)-Gallocatechin gallate and rhodiosin were identified as inhibitors with Kis of 2.47 μM and 73.38 μM, respectively. Molecular docking and isothermal titration calorimetry showed that both inhibitors interact with SaSDH with a KD of 44.65 μM for (-)-gallocatechin gallate and 16.45 μM for rhodiosin. Both inhibitors had antibacterial activity, showing MICs of 50 μg/mL for (-)-gallocatechin gallate and 250 μg/mL for rhodiosin against S. aureus. The current findings have the potential for identification of drugs to treat S. aureus infections by targeting SaSDH.
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Affiliation(s)
- Mengfan Zhu
- Department of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Jinfeng Qu
- Department of Pharmacy, Fujian Medical University, Fuzhou, China
| | - Qi Deng
- Department of Pharmacy, Fujian Medical University, Fuzhou, China
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2
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Morales BGDV, Evaristo JAM, Oliveira GARDE, Garay AFG, Diaz JJAR, Arruda A, Pereira SS, Zanchi FB. Expression and purification of active shikimate dehydrogenase from Plasmodium falciparum. AN ACAD BRAS CIENC 2024; 96:e20230382. [PMID: 38422345 DOI: 10.1590/0001-3765202420230382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 10/02/2023] [Indexed: 03/02/2024] Open
Abstract
Plasmodium falciparum is known to cause severe malaria, current treatment consists in artemisinin-based combination therapy, but resistance can lead to treatment failure. Knowledge concerning P. falciparum essential proteins can be used for searching new antimalarials, among these a potential candidate is shikimate dehydrogenase (SDH), an enzyme part of the shikimate pathway which is responsible for producing endogenous aromatic amino acids. SDH from P. falciparum (PfSDH) is unexplored by the scientific community, therefore, this study aims to establish the first protocol for active PfSDH expression. Putative PfSDH nucleotide sequence was used to construct an optimized expression vector pET28a+PfSDH inserted in E. coli BL21(DE3). As a result, optimal expression conditions were acquired by varying IPTG and temperature through time. Western Blot analysis was applied to verify appropriate PfSDH expression, solubilization and purification started with lysis followed by two-steps IMAC purification. Enzyme activity was measured spectrophotometrically by NADPH oxidation, optimal PfSDH expression occur at 0.1 mM IPTG for 48 hours growing at 37 °C and shaking at 200 rpm, recombinant PfSDH obtained after purification was soluble, pure and its physiological catalysis was confirmed. Thus, this study describes the first protocol for heterologous expression of PfSDH in soluble and active form.
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Affiliation(s)
- Bruno G Dalla Vecchia Morales
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Federal University of Rondonia (UNIR), BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- São Lucas University Center (UniSL), Alexandre Guimarães Street, 1927, Areal, 76804-373 Porto Velho, RO, Brazil
| | - Joseph Albert M Evaristo
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
| | - George A R DE Oliveira
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Oswaldo Cruz Institute (IOC), Brasil Avenue 4365, Manguinhos, 21040-900 Rio de Janeiro, RJ, Brazil
| | - Ana Fidelina G Garay
- Centro para el Desarrollo de la Investigación Científica (CEDIC), P975+F58, Manduvira, Asuncion, Paraguay
| | - Jorge Javier A R Diaz
- Centro para el Desarrollo de la Investigación Científica (CEDIC), P975+F58, Manduvira, Asuncion, Paraguay
| | - Andrelisse Arruda
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Antibodies Engineering, Beira Street, 7671, Lagoa, 76812-245 Porto Velho, RO, Brazil
- Oswaldo Cruz Foundation Brasília (FIOCRUZ BRASÍLIA), L3 North Avenue, Gleba A, 70904-130 Brasília, DF, Brazil
| | - Soraya S Pereira
- Federal University of Rondonia (UNIR), BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Antibodies Engineering, Beira Street, 7671, Lagoa, 76812-245 Porto Velho, RO, Brazil
| | - Fernando B Zanchi
- Oswaldo Cruz Foundation Rondônia (FIOCRUZ/RO), Laboratory of Bioinformatics and Medicinal Chemistry, BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Federal University of Rondonia (UNIR), BR 364, km 9,5, Centro, 76801-059 Porto Velho, RO, Brazil
- Oswaldo Cruz Institute (IOC), Brasil Avenue 4365, Manguinhos, 21040-900 Rio de Janeiro, RJ, Brazil
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Lee CH, Kim S, Seo H, Kim KJ. Structural and Biochemical Analysis of 3-Dehydroquinate Dehydratase from Corynebacterium glutamicum. J Microbiol Biotechnol 2023; 33:1595-1605. [PMID: 38151830 PMCID: PMC10772564 DOI: 10.4014/jmb.2305.05018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 12/29/2023]
Abstract
Dehydroquinate dehydratase (DHQD) catalyzes the conversion of 3-dehydroquinic acid (DHQ) into 3-dehydroshikimic acid in the mid stage of the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids and folates. Here, we report two the crystal structures of type II DHQD (CgDHQD) derived from Corynebacterium glutamicum, which is a widely used industrial platform organism. We determined the structures for CgDHQDWT with the citrate at a resolution of 1.80Å and CgDHQDR19A with DHQ complexed forms at a resolution of 2.00 Å, respectively. The enzyme forms a homododecamer consisting of four trimers with three interfacial active sites. We identified the DHQ-binding site of CgDHQD and observed an unusual binding mode of citrate inhibitor in the site with a half-opened lid loop. A structural comparison of CgDHQD with a homolog derived from Streptomyces coelicolor revealed differences in the terminal regions, lid loop, and active site. Particularly, CgDHQD, including some Corynebacterium species, possesses a distinctive residue P105, which is not conserved in other DHQDs at the position near the 5-hydroxyl group of DHQ. Replacements of P105 with isoleucine and valine, conserved in other DHQDs, caused an approximately 70% decrease in the activity, but replacement of S103 with threonine (CgDHQDS103T) caused a 10% increase in the activity. Our biochemical studies revealed the importance of key residues and enzyme kinetics for wild type and CgDHQDS103T, explaining the effect of the variation. This structural and biochemical study provides valuable information for understanding the reaction efficiency that varies due to structural differences caused by the unique sequences of CgDHQD.
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Affiliation(s)
- Chan Hwi Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sangwoo Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hogyun Seo
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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Zhang C, Guo X, Wang H, Dai X, Yan B, Wang S, Guo L. Induction and metabolomic analysis of hairy roots of Atractylodes lancea. Appl Microbiol Biotechnol 2023; 107:6655-6670. [PMID: 37688598 DOI: 10.1007/s00253-023-12735-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/26/2023] [Accepted: 08/20/2023] [Indexed: 09/11/2023]
Abstract
Atractylodes lancea is an important source of traditional Chinese medicines. Sesquiterpenoids are the key active compounds in A. lancea, and their presence determines the quality of the material. Hairy hoot (HR) culture is a potential method to produce medicinally active compounds industrially; however, the induction and metabolic profiling of A. lancea HR have not been reported. We found that optimal induction of A. lancea HR was achieved by Agrobacterium rhizogenes strain C58C1 using the young leaves of tissue culture seedlings in the rooting stage as explants. Ultra-performance liquid chromatography-tandem mass spectrometric analyses of the chemical compositions of HR and normal root (NR) led to the annotation of 1046 metabolites. Over 200 differentially accumulated metabolites were identified, with 41 found to be up-regulated in HR relative to NR and 179 down-regulated in HR. Specifically, atractylodin levels were higher in HR, while the levels of β-eudesmol and hinesol were higher in NR. Metabolic pathway analyses showed a significant difference in metabolites of the shikimate acid pathway between HR and NR. Five A. lancea compounds are potential biomarkers for evaluation of HR and NR quality. This study provides an important reference for the application of HR for the production of medicinally active compounds. KEY POINTS: • We established an efficient protocol for the induction of HR in A. lancea • HR was found to have a significantly higher amount of atractylodin than did NRs • Metabolic pathway analyses showed a significant difference in metabolites of the shikimate acid pathway between HR and NR.
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Affiliation(s)
- Chengcai Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Xiuzhi Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Hongyang Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
| | - Xiaoyu Dai
- Dexing Research and Training Center of Chinese Medical Sciences, Dexing, 334220, People's Republic of China
| | - Binbin Yan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China
- Dexing Research and Training Center of Chinese Medical Sciences, Dexing, 334220, People's Republic of China
| | - Sheng Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China.
- Dexing Research and Training Center of Chinese Medical Sciences, Dexing, 334220, People's Republic of China.
| | - Lanping Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, People's Republic of China.
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Pratyusha DS, Sarada DVL. MYB transcription factors-master regulators of phenylpropanoid biosynthesis and diverse developmental and stress responses. PLANT CELL REPORTS 2022; 41:2245-2260. [PMID: 36171500 DOI: 10.1007/s00299-022-02927-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Phenylpropanoids, the largest class of natural products including flavonoids, anthocyanins, monolignols and tannins perform multiple functions ranging from photosynthesis, nutrient uptake, regulating growth, cell division, maintenance of redox homeostasis and biotic and abiotic stress responses. Being sedentary life forms, plants possess several regulatory modules that increase their performance in varying environments by facilitating activation of several signaling cascades upon perception of developmental and stress signals. Of the various regulatory modules, those involving MYB transcription factors are one of the extensive groups involved in regulating the phenylpropanoid metabolic enzymes in addition to other genes. R2R3 MYB transcription factors are a class of plant-specific transcription factors that regulate the expression of structural genes involved in anthocyanin, flavonoid and monolignol biosynthesis which are indispensable to several developmental pathways and stress responses. The aim of this review is to present the regulation of the phenylpropanoid pathway by MYB transcription factors via Phospholipase D/phosphatidic acid signaling, downstream activation of the structural genes, leading to developmental and/or stress responses. Specific MYB transcription factors inducing or repressing specific structural genes of anthocyanin, flavonoid and lignin biosynthetic pathways are discussed. Further the roles of MYB in activating biotic and abiotic stress responses are delineated. While several articles have reported the role of MYB's in stress responses, they are restricted to two or three specific MYB factors. This review is a consolidation of the diverse roles of different MYB transcription factors involved both in induction and repression of anthocyanin, flavonoid, and lignin biosynthesis.
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Affiliation(s)
- Durvasula Sumana Pratyusha
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603 203, India
| | - Dronamraju V L Sarada
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603 203, India.
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Metabolic Engineering of Shikimic Acid Biosynthesis Pathway for the Production of Shikimic Acid and Its Branched Products in Microorganisms: Advances and Prospects. Molecules 2022; 27:molecules27154779. [PMID: 35897952 PMCID: PMC9332510 DOI: 10.3390/molecules27154779] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
The shikimate pathway is a necessary pathway for the synthesis of aromatic compounds. The intermediate products of the shikimate pathway and its branching pathway have promising properties in many fields, especially in the pharmaceutical industry. Many important compounds, such as shikimic acid, quinic acid, chlorogenic acid, gallic acid, pyrogallol, catechol and so on, can be synthesized by the shikimate pathway. Among them, shikimic acid is the key raw material for the synthesis of GS4104 (Tamiflu®), an inhibitor of neuraminidase against avian influenza virus. Quininic acid is an important intermediate for synthesis of a variety of raw chemical materials and drugs. Gallic acid and catechol receive widespread attention as pharmaceutical intermediates. It is one of the hotspots to accumulate many kinds of target products by rationally modifying the shikimate pathway and its branches in recombinant strains by means of metabolic engineering. This review considers the effects of classical metabolic engineering methods, such as central carbon metabolism (CCM) pathway modification, key enzyme gene modification, blocking the downstream pathway on the shikimate pathway, as well as several expansion pathways and metabolic engineering strategies of the shikimate pathway, and expounds the synthetic biology in recent years in the application of the shikimate pathway and the future development direction.
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Jalal K, Khan K, Hassam M, Abbas MN, Uddin R, Khusro A, Sahibzada MUK, Gajdács M. Identification of a Novel Therapeutic Target against XDR Salmonella Typhi H58 Using Genomics Driven Approach Followed Up by Natural Products Virtual Screening. Microorganisms 2021; 9:2512. [PMID: 34946114 PMCID: PMC8708826 DOI: 10.3390/microorganisms9122512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022] Open
Abstract
Typhoid fever is caused by a pathogenic, rod-shaped, flagellated, and Gram-negative bacterium known as Salmonella Typhi. It features a polysaccharide capsule that acts as a virulence factor and deceives the host immune system by protecting phagocytosis. Typhoid fever remains a major health concern in low and middle-income countries, with an estimated death rate of ~200,000 per annum. However, the situation is exacerbated by the emergence of the extensively drug-resistant (XDR) strain designated as H58 of S. Typhi. The emergence of the XDR strain is alarming, and it poses serious threats to public health due to the failure of the current therapeutic regimen. A relatively newer computational method called subtractive genomics analyses has been widely applied to discover novel and new drug targets against pathogens, particularly drug-resistant ones. The method involves the gradual reduction of the complete proteome of the pathogen, leading to few potential and novel drug targets. Thus, in the current study, a subtractive genomics approach was applied against the Salmonella XDR strain to identify potential drug targets. The current study predicted four prioritized proteins (i.e., Colanic acid biosynthesis acetyltransferase wcaB, Shikimate dehydrogenase aroE, multidrug efflux RND transporter permease subunit MdtC, and pantothenate synthetase panC) as potential drug targets. Though few of the prioritized proteins are treated in the literature as the established drug targets against other pathogenic bacteria, these drug targets are identified here for the first time against S. Typhi (i.e., S. Typhi XDR). The current study aimed at drawing attention to new drug targets against S. Typhi that remain largely unexplored. One of the prioritized drug targets, i.e., Colanic acid biosynthesis acetyltransferase, was predicted as a unique, new drug target against S. Typhi XDR. Therefore, the Colanic acid was further explored using structure-based techniques. Additionally, ~1000 natural compounds were docked with Colanic acid biosynthesis acetyltransferase, resulting in the prediction of seven compounds as potential lead candidates against the S. Typhi XDR strain. The ADMET properties and binding energies via the docking program of these seven compounds characterized them as novel drug candidates. They may potentially be used for the development of future drugs in the treatment of Typhoid fever.
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Affiliation(s)
- Khurshid Jalal
- International Center for Chemical and Biological Science, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi 75270, Pakistan;
| | - Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi 75270, Pakistan; (K.K.); (M.H.)
| | - Muhammad Hassam
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi 75270, Pakistan; (K.K.); (M.H.)
| | - Muhammad Naseer Abbas
- Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan;
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi 75270, Pakistan; (K.K.); (M.H.)
| | - Ameer Khusro
- Research Department of Plant Biology and Biotechnology, Loyola College, Chennai 600034, India;
| | | | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, 6720 Szeged, Hungary
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Hýsková V, Bělonožníková K, Šmeringaiová I, Kavan D, Ingr M, Ryšlavá H. How is the activity of shikimate dehydrogenase from the root of Petroselinum crispum (parsley) regulated and which side reactions are catalyzed? PHYTOCHEMISTRY 2021; 190:112881. [PMID: 34365296 DOI: 10.1016/j.phytochem.2021.112881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/18/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Inhibitors of the shikimate pathway are widely used as herbicides, antibiotics, and anti-infectious drugs. However, the regulation of the shikimic pathway is complex, and little is known about the feedback regulation of the shikimate dehydrogenase (SDH, EC 1.1.1.25) in plants. Thus, the aim of this study was to elucidate the kinetic mechanism of SDH purified from the root of Petroselinum crispum (parsley), to determine all possible reaction products and to identify phenylpropanoid compounds that affect its activity. Our results showed that the bisubstrate reaction catalyzed by P. crispum SDH follows a sequential ordered mechanism, except for three dead-end complexes. The main and lateral reactions of SDH were monitored by mass spectrometry, thereby detecting protocatechuic acid as a byproduct. Gallic acid was formed non-enzymatically, whereas quinate was not detected. Several polyphenolic compounds inhibited SDH activity, especially tannic, caffeic and chlorogenic acids, with IC50 0.014 mM, 0.15 mM, and 0.19 mM, respectively. The number of hydroxyl groups influenced their inhibition effect on SDH, and p-coumaric, t-ferulic, sinapic, syringic and salicylic acids were less effective SDH inhibitors. Nevertheless, one branch of the phenylpropanoid pathway may affect SDH activity through feedback regulation.
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Affiliation(s)
- Veronika Hýsková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 40, Czech Republic.
| | - Kateřina Bělonožníková
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 40, Czech Republic.
| | - Ingrida Šmeringaiová
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 40, Czech Republic.
| | - Daniel Kavan
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 40, Czech Republic.
| | - Marek Ingr
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 40, Czech Republic; Tomas Bata University in Zlín, Faculty of Technology, Department of Physics and Materials Engineering, Nám. T.G. Masaryka 5555, 760 01, Zlín, Czech Republic.
| | - Helena Ryšlavá
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 40, Czech Republic.
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MohammadiPeyhani H, Chiappino-Pepe A, Haddadi K, Hafner J, Hadadi N, Hatzimanikatis V. NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism. eLife 2021; 10:e65543. [PMID: 34340747 PMCID: PMC8331181 DOI: 10.7554/elife.65543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 07/07/2021] [Indexed: 12/30/2022] Open
Abstract
The discovery of a drug requires over a decade of intensive research and financial investments - and still has a high risk of failure. To reduce this burden, we developed the NICEdrug.ch resource, which incorporates 250,000 bioactive molecules, and studied their enzymatic metabolic targets, fate, and toxicity. NICEdrug.ch includes a unique fingerprint that identifies reactive similarities between drug-drug and drug-metabolite pairs. We validated the application, scope, and performance of NICEdrug.ch over similar methods in the field on golden standard datasets describing drugs and metabolites sharing reactivity, drug toxicities, and drug targets. We use NICEdrug.ch to evaluate inhibition and toxicity by the anticancer drug 5-fluorouracil, and suggest avenues to alleviate its side effects. We propose shikimate 3-phosphate for targeting liver-stage malaria with minimal impact on the human host cell. Finally, NICEdrug.ch suggests over 1300 candidate drugs and food molecules to target COVID-19 and explains their inhibitory mechanism for further experimental screening. The NICEdrug.ch database is accessible online to systematically identify the reactivity of small molecules and druggable enzymes with practical applications in lead discovery and drug repurposing.
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Affiliation(s)
- Homa MohammadiPeyhani
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Kiandokht Haddadi
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Jasmin Hafner
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Noushin Hadadi
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFLLausanneSwitzerland
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Lee HN, Seo SY, Kim HJ, Park JH, Park E, Choi SS, Lee SJ, Kim ES. Artificial cell factory design for shikimate production in Escherichia coli. J Ind Microbiol Biotechnol 2021; 48:6316114. [PMID: 34227672 PMCID: PMC8788726 DOI: 10.1093/jimb/kuab043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/26/2021] [Indexed: 11/13/2022]
Abstract
Shikimate is a key intermediate in high-demand for synthesizing valuable antiviral drugs, such as the anti-influenza drug, oseltamivir (Tamiflu®). Microbial-based shikimate production strategies have been developed to overcome the unstable and expensive supply of shikimate derived from traditional plant extraction processes. Although shikimate biosynthesis has been reported in several engineered bacterial species, the shikimate production yield is still unsatisfactory. This study designed an Escherichia coli cell factory and optimized the fed-batch culture process to achieve a high titer of shikimate production. Using the previously constructed dehydroshikimate (DHS)-overproducing E. coli strain, two genes (aroK and aroL) responsible for converting shikimate to the next step were disrupted to facilitate shikimate accumulation. The genes with negative effects on shikimate biosynthesis, including tyrR, ptsG, and pykA, were disrupted. In contrast, several shikimate biosynthetic pathway genes, including aroB, aroD, aroF, aroG, and aroE, were overexpressed to maximize the glucose uptake and intermediate flux. The shiA involved in shikimate transport was disrupted, and the tktA involved in the accumulation of both PEP and E4P was overexpressed. The rationally designed shikimate-overproducing E. coli strain grown in an optimized medium produced approximately 101 g/L of shikimate in 7-L fed-batch fermentation, which is the highest level of shikimate production reported thus far. Overall, rational cell factory design and culture process optimization for microbial-based shikimate production will play a key role in complementing traditional plant-derived shikimate production processes.
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Affiliation(s)
- Han-Na Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea.,STR Biotech Co., Ltd., Bioplaza 4-3, 56, Soyanggang-ro, Chuncheon-si, Gangwon-do 24232, Republic of Korea
| | - Seung-Yeul Seo
- STR Biotech Co., Ltd., Bioplaza 4-3, 56, Soyanggang-ro, Chuncheon-si, Gangwon-do 24232, Republic of Korea
| | - Hey-Jin Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Ji-Hoon Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Eunhwi Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Si-Sun Choi
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Sang Joung Lee
- STR Biotech Co., Ltd., Bioplaza 4-3, 56, Soyanggang-ro, Chuncheon-si, Gangwon-do 24232, Republic of Korea
| | - Eung-Soo Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
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11
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Batory M, Rotsztejn H. Shikimic acid in the light of current knowledge. J Cosmet Dermatol 2021; 21:501-505. [PMID: 33825313 DOI: 10.1111/jocd.14136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/27/2021] [Accepted: 04/02/2021] [Indexed: 01/03/2023]
Abstract
Shikimic acid (SA) has been mainly used in the pharmaceutical industry for production of drugs, however, recently it has also appeared in the world of cosmetics. So far, there have not been many publications on cosmetics containing SA or research studies on the compound, especially those that would involve testing cosmetic products on subjects. The main source of SA is star anise. The recommended concentration of SA in cosmetic preparations ranges between 1 and 5%. The pH of a 5% solution of SA in water is 3. SA at a concentration of 5% has a similar exfoliative effect to that of 50% glycolic acid. It shows antiviral, exfoliating, deodorizing, anti-acne, anti-dandruff, whitening and moisturizing activity. It also regulates the amount of secreted sebum, moreover, it has antibacterial, anti-inflammatory, hair-growth stimulating, anti-aging effect and antifungal properties.
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Affiliation(s)
- Mirella Batory
- Department of Cosmetology and Aesthetic Dermatology, Faculty of Pharmacy, Medical University of Lodz, Lodz, Poland
| | - Helena Rotsztejn
- Department of Cosmetology and Aesthetic Dermatology, Faculty of Pharmacy, Medical University of Lodz, Lodz, Poland
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12
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Xu Q, Liang P, Lu H, Jin S, Dong Y, Zhang J. Design, Synthesis and Bioactivity of Fluopyram Derivatives Containing Diamide Moiety. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202103021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Kadosh E, Snir-Alkalay I, Venkatachalam A, May S, Lasry A, Elyada E, Zinger A, Shaham M, Vaalani G, Mernberger M, Stiewe T, Pikarsky E, Oren M, Ben-Neriah Y. The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic. Nature 2020; 586:133-138. [PMID: 32728212 PMCID: PMC7116712 DOI: 10.1038/s41586-020-2541-0] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/01/2020] [Indexed: 12/16/2022]
Abstract
Somatic mutations in p53, which inactivate the tumour-suppressor function of p53 and often confer oncogenic gain-of-function properties, are very common in cancer1,2. Here we studied the effects of hotspot gain-of-function mutations in Trp53 (the gene that encodes p53 in mice) in mouse models of WNT-driven intestinal cancer caused by Csnk1a1 deletion3,4 or ApcMin mutation5. Cancer in these models is known to be facilitated by loss of p533,6. We found that mutant versions of p53 had contrasting effects in different segments of the gut: in the distal gut, mutant p53 had the expected oncogenic effect; however, in the proximal gut and in tumour organoids it had a pronounced tumour-suppressive effect. In the tumour-suppressive mode, mutant p53 eliminated dysplasia and tumorigenesis in Csnk1a1-deficient and ApcMin/+ mice, and promoted normal growth and differentiation of tumour organoids derived from these mice. In these settings, mutant p53 was more effective than wild-type p53 at inhibiting tumour formation. Mechanistically, the tumour-suppressive effects of mutant p53 were driven by disruption of the WNT pathway, through preventing the binding of TCF4 to chromatin. Notably, this tumour-suppressive effect was completely abolished by the gut microbiome. Moreover, a single metabolite derived from the gut microbiota–gallic acid–could reproduce the entire effect of the microbiome. Supplementing gut-sterilized p53-mutant mice and p53-mutant organoids with gallic acid reinstated the TCF4–chromatin interaction and the hyperactivation of WNT, thus conferring a malignant phenotype to the organoids and throughout the gut. Our study demonstrates the substantial plasticity of a cancer mutation and highlights the role of the microenvironment in determining its functional outcome.
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Affiliation(s)
- Eliran Kadosh
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Irit Snir-Alkalay
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Avanthika Venkatachalam
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Shahaf May
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Audrey Lasry
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Ela Elyada
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Adar Zinger
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maya Shaham
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gitit Vaalani
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Marco Mernberger
- Institute of Molecular Oncology, Genomics Core Facility, Philipps University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Genomics Core Facility, Philipps University Marburg, Marburg, Germany
| | - Eli Pikarsky
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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Li Z, Wang H, Ding D, Liu Y, Fang H, Chang Z, Chen T, Zhang D. Metabolic engineering of Escherichia coli for production of chemicals derived from the shikimate pathway. ACTA ACUST UNITED AC 2020; 47:525-535. [DOI: 10.1007/s10295-020-02288-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022]
Abstract
Abstract
The shikimate pathway is indispensable for the biosynthesis of natural products with aromatic moieties. These products have wide current and potential applications in food, cosmetics and medicine, and consequently have great commercial value. However, compounds extracted from various plants or synthesized from petrochemicals no longer satisfy the requirements of contemporary industries. As a result, an increasing number of studies has focused on this pathway to enable the biotechnological manufacture of natural products, especially in E. coli. Furthermore, the development of synthetic biology, systems metabolic engineering and high flux screening techniques has also contributed to improving the biosynthesis of high-value compounds based on the shikimate pathway. Here, we review approaches based on a combination of traditional and new metabolic engineering strategies to increase the metabolic flux of the shikimate pathway. In addition, applications of this optimized pathway to produce aromatic amino acids and a range of natural products is also elaborated. Finally, this review sums up the opportunities and challenges facing this field.
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Affiliation(s)
- Zhu Li
- grid.33763.32 0000 0004 1761 2484 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education); SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin China
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Huiying Wang
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Dongqin Ding
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.410726.6 0000 0004 1797 8419 University of Chinese Academy of Sciences 100049 Beijing China
| | - Yongfei Liu
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Huan Fang
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
| | - Zhishuai Chang
- grid.33763.32 0000 0004 1761 2484 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education); SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin China
| | - Tao Chen
- grid.33763.32 0000 0004 1761 2484 Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education); SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology Tianjin University 300072 Tianjin China
| | - Dawei Zhang
- grid.9227.e 0000000119573309 Key Laboratory of Systems Microbial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.9227.e 0000000119573309 Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences 300308 Tianjin China
- grid.410726.6 0000 0004 1797 8419 University of Chinese Academy of Sciences 100049 Beijing China
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15
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Xing SC, Mi JD, Chen JY, Hu JX, Liao XD. Metabolic activity of Bacillus coagulans R11 and the health benefits of and potential pathogen inhibition by this species in the intestines of laying hens under lead exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:134507. [PMID: 31881475 DOI: 10.1016/j.scitotenv.2019.134507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/19/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Probiotics are widely used in agricultural breeding for care and maintenance of animal health, especially Bacillus coagulans, a new and popular species that could replace Lactobacillus. However, lead contamination in feed might influence the beneficial function. In the present study, Bacillus coagulans R11 was used as a model bacterium to investigate the effect of lead on changes in metabolites and genes, which could influence the beneficial function on laying hen. At the laboratory scale, transcriptomics and metabolomics were used to screen the main metabolites and related genes under lead exposure. The results showed that 4-acetamidobutanoic acid, dodecanoic acid, L-3-phenyllactic acid, apigenin and daidzein, which are antioxidants and antibacterial agents, were the main metabolites, even in the 100 ppm lead exposure group (the levels of these metabolites were 1.17-, 1.10-, 4.80-, 1.43- and 1.67-fold higher in the 100 ppm group than in pure culture medium). Twenty-three genes associated with the syntheses of the above 5 main metabolites were identified. Further animal experiments showed that B. coagulans R11 feeding of laying hens under lead exposure could prevent oxidative damage by increasing T-AOC and T-SOD activity and reducing the MDA concentration in serum and reducing the abundances of potential pathogens (Escherichia coli, Pseudomonas aeruginosa and Salmonella). Further analysis also showed that the inhibition of pathogen growth was due to the regulation of gene expression, as observed by transcriptomics, and these genes were associated with the abovementioned 5 main metabolites. However, the laying rate decreased by 10.53% compared with that of the control group when the lead exposure concentration was 100 mg/kg. The present study suggested that Bacillus coagulans R11 could help prevent oxidative damage and inhibit pathogen growth in laying hens to maintain a healthy intestinal environment for daily breeding, but under high-lead conditions, Bacillus coagulans R11 feeding could decrease the laying rate.
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Affiliation(s)
- Si-Cheng Xing
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Dui Mi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jing-Yuan Chen
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jia-Xin Hu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xin-Di Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry Agriculture, Guangzhou 510642, Guangdong, China; National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou 510642, Guangdong, China.
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16
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Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs. Molecules 2020; 25:molecules25061259. [PMID: 32168746 PMCID: PMC7144000 DOI: 10.3390/molecules25061259] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Roughly a third of the world’s population is estimated to have latent Mycobacterium tuberculosis infection, being at risk of developing active tuberculosis (TB) during their lifetime. Given the inefficacy of prophylactic measures and the increase of drug-resistant M. tuberculosis strains, there is a clear and urgent need for the development of new and more efficient chemotherapeutic agents, with selective toxicity, to be implemented on patient treatment. The component enzymes of the shikimate pathway, which is essential in mycobacteria and absent in humans, stand as attractive and potential targets for the development of new drugs to treat TB. This review gives an update on published work on the enzymes of the shikimate pathway and some insight on what can be potentially explored towards selective drug development.
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17
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Silver RJ, Paczosa MK, McCabe AL, Balada-Llasat JM, Baleja JD, Mecsas J. Amino Acid Biosynthetic Pathways Are Required for Klebsiella pneumoniae Growth in Immunocompromised Lungs and Are Druggable Targets during Infection. Antimicrob Agents Chemother 2019; 63:e02674-18. [PMID: 31109974 PMCID: PMC6658747 DOI: 10.1128/aac.02674-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/11/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of multidrug-resistant Klebsiella pneumoniae has rendered a large array of infections difficult to treat. In a high-throughput genetic screen of factors required for K. pneumoniae survival in the lung, amino acid biosynthesis genes were critical for infection in both immunosuppressed and wild-type (WT) mice. The limited pool of amino acids in the lung did not change during infection and was insufficient for K. pneumoniae to overcome attenuating mutations in aroA, hisA, leuA, leuB, serA, serB, trpE, and tyrA in WT and immunosuppressed mice. Deletion of aroA, which encodes 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase class I, resulted in the most severe attenuation. Treatment with the EPSP synthase-specific competitive inhibitor glyphosate decreased K. pneumoniae growth in the lungs. K. pneumoniae expressing two previously identified glyphosate-resistant mutations in EPSP synthase had significant colonization defects in lung infection. Selection and characterization of six spontaneously glyphosate-resistant mutants in K. pneumoniae yielded no mutations in aroA Strikingly, glyphosate treatment of mice lowered the bacterial burden of two of three spontaneous glyphosate-resistant mutants and further lowered the burden of the less-attenuated EPSP synthase catalytic mutant. Of 39 clinical isolate strains, 9 were resistant to glyphosate at levels comparable to those of selected resistant strains, and none appeared to be more highly resistant. These findings demonstrate amino acid biosynthetic pathways essential for K. pneumoniae infection are promising novel therapeutic targets.
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Affiliation(s)
- Rebecca J Silver
- Graduate Program in Immunology, MERGE-ID Track, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Michelle K Paczosa
- Graduate Program in Immunology, MERGE-ID Track, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Anne L McCabe
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | | | - James D Baleja
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Joan Mecsas
- Graduate Program in Immunology, MERGE-ID Track, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
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18
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Candeias NR, Assoah B, Simeonov SP. Production and Synthetic Modifications of Shikimic Acid. Chem Rev 2018; 118:10458-10550. [PMID: 30350584 DOI: 10.1021/acs.chemrev.8b00350] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Shikimic acid is a natural product of industrial importance utilized as a precursor of the antiviral Tamiflu. It is nowadays produced in multihundred ton amounts from the extraction of star anise ( Illicium verum) or by fermentation processes. Apart from the production of Tamiflu, shikimic acid has gathered particular notoriety as its useful carbon backbone and inherent chirality provide extensive use as a versatile chiral precursor in organic synthesis. This review provides an overview of the main synthetic and microbial methods for production of shikimic acid and highlights selected methods for isolation from available plant sources. Furthermore, we have attempted to demonstrate the synthetic utility of shikimic acid by covering the most important synthetic modifications and related applications, namely, synthesis of Tamiflu and derivatives, synthetic manipulations of the main functional groups, and its use as biorenewable material and in total synthesis. Given its rich chemistry and availability, shikimic acid is undoubtedly a promising platform molecule for further exploration. Therefore, in the end, we outline some challenges and promising future directions.
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Affiliation(s)
- Nuno R Candeias
- Laboratory of Chemistry and Bioengineering , Tampere University of Technology , Korkeakoulunkatu 8 , 33101 Tampere , Finland
| | - Benedicta Assoah
- Laboratory of Chemistry and Bioengineering , Tampere University of Technology , Korkeakoulunkatu 8 , 33101 Tampere , Finland
| | - Svilen P Simeonov
- Laboratory Organic Synthesis and Stereochemistry, Institute of Organic Chemistry with Centre of Phytochemistry , Bulgarian Academy of Sciences , Acad. G. Bontchev str. Bl. 9 , 1113 Sofia , Bulgaria
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Bilal M, Wang S, Iqbal HMN, Zhao Y, Hu H, Wang W, Zhang X. Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments. Appl Microbiol Biotechnol 2018; 102:7759-7773. [PMID: 30014168 DOI: 10.1007/s00253-018-9222-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 02/08/2023]
Abstract
Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods. Metabolic engineering allows elevated shikimate production titer by inactivating the competing pathways, increasing intracellular level of key precursors, and overexpressing rate-limiting enzymes. The development of synthetic and systems biology-based novel technologies have revealed a new roadmap for the construction of high shikimate-producing strains. This review elaborates the enhanced biosynthesis of shikimate by utilizing an array of traditional metabolic engineering along with novel advanced technologies. The first part of the review is focused on the mechanistic pathway for shikimate production, use of recombinant and engineered strains, improving metabolic flux through the shikimate pathway, chemically inducible chromosomal evolution, and bioprocess engineering strategies. The second part discusses a variety of industrially pertinent compounds derived from shikimate with special reference to aromatic amino acids and phenazine compound, and main engineering strategies for their production in diverse bacterial strains. Towards the end, the work is wrapped up with concluding remarks and future considerations.
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Affiliation(s)
- Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, NL, Mexico
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Santosh R, Selvam MK, Kanekar SU, Nagaraja GK. Synthesis, Characterization, Antibacterial and Antioxidant Studies of Some Heterocyclic Compounds from Triazole‐Linked Chalcone Derivatives. ChemistrySelect 2018. [DOI: 10.1002/slct.201800905] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Rangappa Santosh
- Department of Studies in ChemistryMangalore University Mangaluru, Karnataka India
| | - Mukunthan K. Selvam
- Department of BiotechnologyManipal Institute of TechnologyManipal Academy of Higher Education Manipal, Karnataka India
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