1
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Stegmüller J, Rodríguez Estévez M, Shu W, Gläser L, Myronovskyi M, Rückert-Reed C, Kalinowski J, Luzhetskyy A, Wittmann C. Systems metabolic engineering of the primary and secondary metabolism of Streptomyces albidoflavus enhances production of the reverse antibiotic nybomycin against multi-resistant Staphylococcus aureus. Metab Eng 2024; 81:123-143. [PMID: 38072358 DOI: 10.1016/j.ymben.2023.12.004] [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: 08/11/2023] [Revised: 11/17/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Nybomycin is an antibiotic compound with proven activity against multi-resistant Staphylococcus aureus, making it an interesting candidate for combating these globally threatening pathogens. For exploring its potential, sufficient amounts of nybomycin and its derivatives must be synthetized to fully study its effectiveness, safety profile, and clinical applications. As native isolates only accumulate low amounts of the compound, superior producers are needed. The heterologous cell factory S. albidoflavus 4N24, previously derived from the cluster-free chassis S. albidoflavus Del14, produced 860 μg L-1 of nybomycin, mainly in the stationary phase. A first round of strain development modulated expression of genes involved in supply of nybomycin precursors under control of the common Perm* promoter in 4N24, but without any effect. Subsequent studies with mCherry reporter strains revealed that Perm* failed to drive expression during the product synthesis phase but that use of two synthetic promoters (PkasOP* and P41) enabled strong constitutive expression during the entire process. Using PkasOP*, several rounds of metabolic engineering successively streamlined expression of genes involved in the pentose phosphate pathway, the shikimic acid pathway, supply of CoA esters, and nybomycin biosynthesis and export, which more than doubled the nybomycin titer to 1.7 mg L-1 in the sixth-generation strain NYB-6B. In addition, we identified the minimal set of nyb genes needed to synthetize the molecule using single-gene-deletion strains. Subsequently, deletion of the regulator nybW enabled nybomycin production to begin during the growth phase, further boosting the titer and productivity. Based on RNA sequencing along the created strain genealogy, we discovered that the nyb gene cluster was unfavorably downregulated in all advanced producers. This inspired removal of a part and the entire set of the four regulatory genes at the 3'-end nyb of the cluster. The corresponding mutants NYB-8 and NYB-9 exhibited marked further improvement in production, and the deregulated cluster was combined with all beneficial targets from primary metabolism. The best strain, S. albidoflavus NYB-11, accumulated up to 12 mg L-1 nybomycin, fifteenfold more than the basic strain. The absence of native gene clusters in the host and use of a lean minimal medium contributed to a selective production process, providing an important next step toward further development of nybomycin.
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Affiliation(s)
- Julian Stegmüller
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andriy Luzhetskyy
- Department of Pharmaceutical Biotechnology, Saarland University, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany.
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2
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Sumii Y, Kamiya K, Nakamura T, Tanaka K, Kaji T, Mukomura J, Kotoku N, Arai M. Study of the Structure–Activity Relationship of an Anti-Dormant Mycobacterial Substance 3-(Phenethylamino)Demethyl(oxy)aaptamine to Create a Probe Molecule for Detecting Its Target Protein. Mar Drugs 2022; 20:md20020098. [PMID: 35200628 PMCID: PMC8879696 DOI: 10.3390/md20020098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/12/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
The current tuberculosis treatment regimen is long and complex, and its failure leads to relapse and emergence of drug resistance. One of the major reasons underlying the extended chemotherapeutic regimen is the ability of Mycobacterium tuberculosis to attain a dormant state. Therefore, the identification of new lead compounds with chemical structures different from those of conventional anti-tuberculosis drugs is essential. The compound 3-(phenethylamino)demethyl(oxy)aaptamine (PDOA, 1), isolated from marine sponge of Aaptos sp., is known as an anti-dormant mycobacterial substance, and has been reported to be effective against the drug resistant strains of M. tuberculosis. However, its target protein still remains unclear. This study aims to clarify the structure–activity relationship of 1 using 15 synthetic analogues, in order to prepare a probe molecule for detecting the target protein of 1. We succeeded in creating the compound 15 with a photoaffinity group that retained antimicrobial activity, which proved to be a suitable probe molecule for identifying the target protein of 1.
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Affiliation(s)
- Yuji Sumii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.S.); (K.K.); (T.N.); (K.T.); (T.K.)
| | - Kentaro Kamiya
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.S.); (K.K.); (T.N.); (K.T.); (T.K.)
| | - Takehiko Nakamura
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.S.); (K.K.); (T.N.); (K.T.); (T.K.)
| | - Kenta Tanaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.S.); (K.K.); (T.N.); (K.T.); (T.K.)
| | - Takumi Kaji
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.S.); (K.K.); (T.N.); (K.T.); (T.K.)
| | - Junya Mukomura
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan;
| | - Naoyuki Kotoku
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.S.); (K.K.); (T.N.); (K.T.); (T.K.)
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan;
- Correspondence: (N.K.); (M.A.); Tel.: +81-77561-4920 (N.K.); +81-66879-8215 (M.A.); Fax: +81-66879-8215 (M.A.)
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; (Y.S.); (K.K.); (T.N.); (K.T.); (T.K.)
- Correspondence: (N.K.); (M.A.); Tel.: +81-77561-4920 (N.K.); +81-66879-8215 (M.A.); Fax: +81-66879-8215 (M.A.)
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3
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Tkachenko AG, Kashevarova NM, Sidorov RY, Nesterova LY, Akhova AV, Tsyganov IV, Vaganov VY, Shipilovskikh SA, Rubtsov AE, Malkov AV. A synthetic diterpene analogue inhibits mycobacterial persistence and biofilm formation by targeting (p)ppGpp synthetases. Cell Chem Biol 2021; 28:1420-1432.e9. [PMID: 33621482 DOI: 10.1016/j.chembiol.2021.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/14/2020] [Accepted: 01/25/2021] [Indexed: 01/23/2023]
Abstract
Bacterial persistence coupled with biofilm formation is directly associated with failure of antibiotic treatment of tuberculosis. We have now identified 4-(4,7-DiMethyl-1,2,3,4-tetrahydroNaphthalene-1-yl)Pentanoic acid (DMNP), a synthetic diterpene analogue, as a lead compound that was capable of suppressing persistence and eradicating biofilms in Mycobacterium smegmatis. By using two reciprocal experimental approaches - ΔrelMsm and ΔrelZ gene knockout mutations versus relMsm and relZ overexpression technique - we showed that both RelMsm and RelZ (p)ppGpp synthetases are plausible candidates for serving as targets for DMNP. In vitro, DMNP inhibited (p)ppGpp-synthesizing activity of purified RelMsm in a concentration-dependent manner. These findings, supplemented by molecular docking simulation, suggest that DMNP targets the structural sites shared by RelMsm, RelZ, and presumably by a few others as yet unidentified (p)ppGpp producers, thereby inhibiting persister cell formation and eradicating biofilms. Therefore, DMNP may serve as a promising lead for development of antimycobacterial drugs.
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Affiliation(s)
- Alexander G Tkachenko
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia.
| | - Natalya M Kashevarova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia
| | - Roman Yu Sidorov
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | - Larisa Yu Nesterova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | - Anna V Akhova
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | - Ivan V Tsyganov
- Laboratory of Microbial Adaptation, Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Russian Academy of Sciences, Ural Branch, Goleva 13, Perm, 614081, Perm Krai, Russia; Perm State University, Bukireva 15, Perm, 614990, Perm Krai, Russia
| | | | | | | | - Andrei V Malkov
- Department of Chemistry, Loughborough University Address: University Road, Loughborough, Leicestershire LE11 3TU, UK.
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4
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Sumii Y, Kotoku N, Han C, Kamiya K, Setiawan A, Vilchèze C, Jacobs WR, Arai M. 3-(Phenethylamino)demethyl(oxy)aaptamine as an anti-dormant mycobacterial substance: Isolation, evaluation and total synthesis. Tetrahedron Lett 2020; 61. [PMID: 32577043 DOI: 10.1016/j.tetlet.2020.151924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
3-(Phenethylamino)demethyl(oxy)aaptamine (1) was re-discovered from the marine sponge of Aaptos sp. as an anti-dormant mycobacterial substance through the bioassay-guided separation. Compound 1 showed potent anti-microbial activity against Mycobacterium bovis BCG with a minimum inhibitory concentration of 0.75 µg/mL under both aerobic conditions and hypoxic conditions inducing dormant state. Compound 1 was also effective against pathogenic M. tuberculosis strains including clinical multidrug-resistant strains. Furthermore, the successful total syntheses of 1 and its analog 3-aminodemethyl(oxy)aaptamine (2) afford sufficient quantities for further biological studies.
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Affiliation(s)
- Yuji Sumii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan.,Present affiliation: Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| | - Naoyuki Kotoku
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan.,Present affiliation: College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Chisu Han
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Kentaro Kamiya
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Andi Setiawan
- Department of Chemistry, Faculty of Science, Lampung University, Jl. Prof. Dr. Sumantri Brodjonegoro No. 1, Bandar Lampung 35145, Indonesia
| | - Catherine Vilchèze
- Albert Einstein College of Medicine; 1301 Morris Park Avenue, Bronx, New York 10461, U.S.A
| | - William R Jacobs
- Albert Einstein College of Medicine; 1301 Morris Park Avenue, Bronx, New York 10461, U.S.A
| | - Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamada-oka, Suita, Osaka 565-0871, Japan
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5
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Yang C, Qian R, Xu Y, Yi J, Gu Y, Liu X, Yu H, Jiao B, Lu X, Zhang W. Marine Actinomycetes-derived Natural Products. Curr Top Med Chem 2020; 19:2868-2918. [PMID: 31724505 DOI: 10.2174/1568026619666191114102359] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/02/2019] [Accepted: 09/22/2019] [Indexed: 12/12/2022]
Abstract
Actinomycetes is an abundant resource for discovering a large number of lead compounds, which play an important role in microbial drug discovery. Compared to terrestrial microorganisms, marine actinomycetes have unique metabolic pathways because of their special living environment, which has the potential to produce a variety of bioactive substances. In this paper, secondary metabolites isolated from marine actinomycetes are reviewed (2013-2018), most of which exhibited cytotoxic, antibacterial, and antiviral biological activities.
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Affiliation(s)
- Chengfang Yang
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Rui Qian
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Yao Xu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Junxi Yi
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Yiwen Gu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Xiaoyu Liu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Haobing Yu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Binghua Jiao
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Xiaoling Lu
- College of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Second Military Medical University, Shanghai, China
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, Australia.,Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, Australia
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6
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Wang X, Elshahawi SI, Ponomareva LV, Ye Q, Liu Y, Copley GC, Hower JC, Hatcher BE, Kharel MK, Van Lanen SG, She QB, Voss SR, Thorson JS, Shaaban KA. Structure Determination, Functional Characterization, and Biosynthetic Implications of Nybomycin Metabolites from a Mining Reclamation Site-Associated Streptomyces. JOURNAL OF NATURAL PRODUCTS 2019; 82:3469-3476. [PMID: 31833370 PMCID: PMC7084111 DOI: 10.1021/acs.jnatprod.9b01015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We report the isolation and characterization of three new nybomycins (nybomycins B-D, 1-3) and six known compounds (nybomycin, 4; deoxynyboquinone, 5; α-rubromycin, 6; β-rubromycin, 7; γ-rubromycin, 8; and [2α(1E,3E),4β]-2-(1,3-pentadienyl)-4-piperidinol, 9) from the Rock Creek (McCreary County, KY) underground coal mine acid reclamation site isolate Streptomyces sp. AD-3-6. Nybomycin D (3) and deoxynyboquinone (5) displayed moderate (3) to potent (5) cancer cell line cytotoxicity and displayed weak to moderate anti-Gram-(+) bacterial activity, whereas rubromycins 6-8 displayed little to no cancer cell line cytotoxicity but moderate to potent anti-Gram-(+) bacterial and antifungal activity. Assessment of the impact of 3 or 5 cancer cell line treatment on 4E-BP1 phosphorylation, a predictive marker of ROS-mediated control of cap-dependent translation, also revealed deoxynyboquinone (5)-mediated downstream inhibition of 4E-BP1p. Evaluation of 1-9 in a recently established axolotl embryo tail regeneration assay also highlighted the prototypical telomerase inhibitor γ-rubromycin (8) as a new inhibitor of tail regeneration. Cumulatively, this work highlights an alternative nybomycin production strain, a small set of new nybomycin metabolites, and previously unknown functions of rubromycins (antifungal activity and inhibition of tail regeneration) and also provides a basis for revision of the previously proposed nybomycin biosynthetic pathway.
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Affiliation(s)
- Xiachang Wang
- Jiangsu Key Laboratory for Functional Substances of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Sherif I. Elshahawi
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
| | - Larissa V. Ponomareva
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Qing Ye
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yang Liu
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Gregory C. Copley
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40511, United States
| | - James C. Hower
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40511, United States
| | - Bruce E. Hatcher
- Division of Water, Kentucky Energy and Environment Cabinet, 2642 Russellville Road, Bowling Green, Kentucky 42101, United States
| | - Madan K. Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Qing-Bai She
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - S. Randal Voss
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky 40536, United States
- Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky 40536, United States
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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7
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New potential drug leads against MDR-MTB: A short review. Bioorg Chem 2019; 95:103534. [PMID: 31884135 DOI: 10.1016/j.bioorg.2019.103534] [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] [Received: 10/03/2019] [Revised: 11/26/2019] [Accepted: 12/20/2019] [Indexed: 12/25/2022]
Abstract
Multidrug resistant Mycobacterium tuberculosis (MDR-MTB) infections have created a critical health problem globally. The appalling rise in drug resistance to all the current therapeutics has triggered the need for identifying new antimycobacterial agents effective against multidrug-resistant Mycobacterium tuberculosis. Structurally unique chemical entities with new mode of action will be required to combat this pressing issue. This review gives an overview of the structures and outlines on various aspects of in vitro pharmacological activities of new antimycobacterial agents, mechanism of action and brief structure activity relationships in the perspective of drug discovery and development. This review also summarizes on recent reports of new antimycobacterial agents.
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8
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Braesel J, Lee JH, Arnould B, Murphy BT, Eustáquio AS. Diazaquinomycin Biosynthetic Gene Clusters from Marine and Freshwater Actinomycetes. JOURNAL OF NATURAL PRODUCTS 2019; 82:937-946. [PMID: 30896942 PMCID: PMC6902439 DOI: 10.1021/acs.jnatprod.8b01028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Tuberculosis is an infectious disease of global concern. Members of the diazaquinomycin (DAQ) class of natural products have shown potent and selective activity against drug-resistant Mycobacterium tuberculosis. However, poor solubility has prevented further development of this compound class. Understanding DAQ biosynthesis may provide a viable route for the generation of derivatives with improved properties. We have sequenced the genomes of two actinomycete bacteria that produce distinct DAQ derivatives. While software tools for automated biosynthetic gene cluster (BGC) prediction failed to detect DAQ BGCs, comparative genomics using MAUVE alignment led to the identification of putative BGCs in the marine Streptomyces sp. F001 and in the freshwater Micromonospora sp. B006. Deletion of the identified daq BGC in strain B006 using CRISPR-Cas9 genome editing abolished DAQ production, providing experimental evidence for BGC assignment. A complete model for DAQ biosynthesis is proposed based on the genes identified. Insufficient knowledge of natural product biosynthesis is one of the major challenges of productive genome mining approaches. The results reported here fill a gap in knowledge regarding the genetic basis for the biosynthesis of DAQ antibiotics. Moreover, identification of the daq BGC shall enable future generations of improved derivatives using biosynthetic methods.
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Affiliation(s)
- Jana Braesel
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jung-Ho Lee
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Benoit Arnould
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian T. Murphy
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alessandra S. Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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9
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Li T, Ding T, Li J. Medicinal Purposes: Bioactive Metabolites from Marine-derived Organisms. Mini Rev Med Chem 2019; 19:138-164. [PMID: 28969543 DOI: 10.2174/1389557517666170927113143] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/25/2017] [Accepted: 06/17/2017] [Indexed: 12/20/2022]
Abstract
The environment of marine occupies about 95% biosphere of the world and it can be a critical source of bioactive compounds for humans to be explored. Special environment such as high salt, high pressure, low temperature, low nutrition and no light, etc. has made the production of bioactive substances different from terrestrial organisms. Natural ingredients secreted by marine-derived bacteria, fungi, actinomycetes, Cyanobacteria and other organisms have been separated as active pharmacophore. A number of evidences have demonstrated that bioactive ingredients isolated from marine organisms can be other means to discover novel medicines, since enormous natural compounds from marine environment were specified to be anticancer, antibacterial, antifungal, antitumor, cytotoxic, cytostatic, anti-inflammatory, antiviral agents, etc. Although considerable progress is being made within the field of chemical synthesis and engineering biosynthesis of bioactive compounds, marine environment still remains the richest and the most diverse sources for new drugs. This paper reviewed the natural compounds discovered recently from metabolites of marine organisms, which possess distinct chemical structures that may form the basis for the synthesis of new drugs to combat resistant pathogens of human life. With developing sciences and technologies, marine-derived bioactive compounds are still being found, showing the hope of solving the problems of human survival and sustainable development of resources and environment.
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Affiliation(s)
- Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, Liaoning, 116600, China
| | - Ting Ding
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,College of Food Science and Technology, Bohai University; Food Safety Key Lab of Liaoning Province; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products; Jinzhou, Liaoning, 121013, China
| | - Jianrong Li
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,College of Food Science and Technology, Bohai University; Food Safety Key Lab of Liaoning Province; National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products; Jinzhou, Liaoning, 121013, China
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10
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Rodríguez Estévez M, Myronovskyi M, Gummerlich N, Nadmid S, Luzhetskyy A. Heterologous Expression of the Nybomycin Gene Cluster from the Marine Strain Streptomyces albus subsp. chlorinus NRRL B-24108. Mar Drugs 2018; 16:md16110435. [PMID: 30400361 PMCID: PMC6265801 DOI: 10.3390/md16110435] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/26/2018] [Accepted: 10/31/2018] [Indexed: 11/16/2022] Open
Abstract
Streptomycetes represent an important reservoir of active secondary metabolites with potential applications in the pharmaceutical industry. The gene clusters responsible for their production are often cryptic under laboratory growth conditions. Characterization of these clusters is therefore essential for the discovery of new microbial pharmaceutical drugs. Here, we report the identification of the previously uncharacterized nybomycin gene cluster from the marine actinomycete Streptomyces albus subsp. chlorinus through its heterologous expression. Nybomycin has previously been reported to act against quinolone-resistant Staphylococcus aureus strains harboring a mutated gyrA gene but not against those with intact gyrA. The nybomycin-resistant mutants generated from quinolone-resistant mutants have been reported to be caused by a back-mutation in the gyrA gene that restores susceptibility to quinolones. On the basis of gene function assignment from bioinformatics analysis, we suggest a model for nybomycin biosynthesis.
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Affiliation(s)
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
| | - Nils Gummerlich
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
| | - Suvd Nadmid
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, 66123 Saarbrücken, Germany.
- Helmholtz-Institut für Pharmazeutische Forschung Saarland, 66123 Saarbrücken, Germany.
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11
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Xu JH, Fan YL, Zhou J. Quinolone-Triazole Hybrids and their Biological Activities. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3234] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jun-Hao Xu
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province; Zhejiang Police College; Hangzhou People's Republic of China
| | - Yi-Lei Fan
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province; Zhejiang Police College; Hangzhou People's Republic of China
| | - Jin Zhou
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province; Zhejiang Police College; Hangzhou People's Republic of China
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12
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Abstract
Covering: 2015. Previous review: Nat. Prod. Rep., 2016, 33, 382-431This review covers the literature published in 2015 for marine natural products (MNPs), with 1220 citations (792 for the period January to December 2015) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1340 in 429 papers for 2015), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.
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Affiliation(s)
- John W Blunt
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Murray H G Munro
- Department of Chemistry, University of Canterbury, Christchurch, New Zealand.
| | - Michèle R Prinsep
- Chemistry, School of Science, University of Waikato, Hamilton, New Zealand
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13
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Abstract
DNA gyrase and topoisomerase IV are type IIA bacterial topoisomerases that are targeted by highly effective antibiotics. However, resistance via multiple mechanisms arises to limit the efficacies of these drugs. Continued research on type IIA bacterial topoisomerases has provided novel approaches to counter the most common resistance mechanism for utilization of these proven targets in antibacterial therapy. Bacterial topoisomerase I is being explored as an alternative target that is not expected to show cross-resistance. Dual targeting or combination therapy could be strategies for circumventing the development of resistance to topoisomerase-targeting antibiotics. Bacterial topoisomerases are high-value bactericidal targets that could continue to be exploited for antibacterial therapy, if new tactics to counter resistance can be adopted.
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14
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Arai M. [Exploring New Drug Targets through the Identification of Target Molecules of Bioactive Natural Products]. YAKUGAKU ZASSHI 2016; 136:669-76. [PMID: 27040348 DOI: 10.1248/yakushi.15-00281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
With the development of cell biology and microbiology, it has become easy to culture many types of animal cells and microbes, and they are frequently used for phenotypic screening to explore medicinal seeds. On the other hand, it is recognized that cells and pathogenic microbes present in pathologic sites and infected regions of the human body display unique properties different from those under general culture conditions. We isolated several bioactive compounds from marine medicinal resources using constructed bioassay-guided separation focusing on the unique changes in the characteristics of cells and pathogenic microbes (Mycobacterium spp.) in the human body under disease conditions. In addition, we also carried out identification studies of target molecules of the bioactive compounds by methods utilizing the gene expression profile, transformants of cells or microbes, synthetic probe molecules of the isolated compounds, etc., since bioactive compounds isolated from the phenotypic screening system often target new molecules. This review presents our phenotypic screening systems, isolation of bioactive compounds from marine medicinal resources, and target identification of bioactive compounds.
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Affiliation(s)
- Masayoshi Arai
- Graduate School of Pharmaceutical Sciences, Osaka University
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