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Cook GD, Stasulli NM. Employing synthetic biology to expand antibiotic discovery. SLAS Technol 2024; 29:100120. [PMID: 38340893 DOI: 10.1016/j.slast.2024.100120] [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: 06/16/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.
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Affiliation(s)
- Greta D Cook
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA
| | - Nikolas M Stasulli
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA.
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2
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Ben Akacha B, Michalak M, Generalić Mekinić I, Kačániová M, Chaari M, Brini F, Ben Saad R, Mnif W, Garzoli S, Ben Hsouna A. Mixture design of α-pinene, α-terpineol, and 1,8-cineole: A multiobjective response followed by chemometric approaches to optimize the antibacterial effect against various bacteria and antioxidant activity. Food Sci Nutr 2024; 12:574-589. [PMID: 38268912 PMCID: PMC10804091 DOI: 10.1002/fsn3.3780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/01/2023] [Accepted: 10/07/2023] [Indexed: 01/26/2024] Open
Abstract
α-Pinene, α-terpineol, and 1,8-cineole are compounds naturally present in essential oils, although their amounts vary from oil to oil. Although several studies have reported their antibacterial and antioxidant effects, there are few reports on the synergistic or antagonistic effects of their combinations. The objective of this study was to investigate the combined antibacterial effect of these three compounds. To our knowledge, this is the first report on the prediction of their optimal combination using the mixture design approach. The experimental antibacterial activity of the α-pinene, α-terpineol, and 1,8-cineole mixtures depended on the proportion of each compound in the mixture and the target strain, with minimum inhibitory concentrations (MIC) ranging from 0.31 to 1.85 mg/mL. Using the increased simplex-centroid mixture design, the mixture containing 0.33% of each molecule proved to be the most effective against Bacillus cereus and had the lowest MIC values. In addition, α-pinene, α-terpineol, and 1,8-cineole showed significant antioxidant activity against 2,2-picryl-1-hydrazyl radical (DPPH), with IC50 values of 24.53 ± 0.05, 65.63 ± 0.71, and 63.58 ± 0.01 μg/mL, respectively. Statistical planning and the development of utility profiles of the substance mixtures can predict the optimal composition that will exhibit the highest antibacterial activity against B. cereus as well as antioxidant properties. Furthermore, the synergistic effect of the mixtures can contribute significantly to their successful use as natural preservatives in various applications.
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Affiliation(s)
- Boutheina Ben Akacha
- Laboratory of Biotechnology and Plant ImprovementCentre of Biotechnology of SfaxSfaxTunisia
| | | | - Ivana Generalić Mekinić
- Department of Food Technology and Biotechnology, Faculty of Chemistry and TechnologyUniversity of SplitSplitCroatia
| | - Miroslava Kačániová
- Faculty of Horticulture, Institute of HorticultureSlovak University of AgricultureNitraSlovakia
| | - Moufida Chaari
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE)Center of Biotechnology of Sfax (CBS)University of SfaxSfaxTunisia
| | - Faical Brini
- Laboratory of Biotechnology and Plant ImprovementCentre of Biotechnology of SfaxSfaxTunisia
| | - Rania Ben Saad
- Laboratory of Biotechnology and Plant ImprovementCentre of Biotechnology of SfaxSfaxTunisia
| | - Wissem Mnif
- Department of Chemistry, College of Sciences at BishaUniversity of BishaBishaSaudi Arabia
| | - Stefania Garzoli
- Department of Chemistry and Technologies of DrugSapienza UniversityRomeItaly
| | - Anis Ben Hsouna
- Laboratory of Biotechnology and Plant ImprovementCentre of Biotechnology of SfaxSfaxTunisia
- Department of Environmental Sciences and Nutrition, Higher Institute of Applied Sciences and Technology of MahdiaUniversity of MonastirMonastirTunisia
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3
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Olukanni OD, Abiola T, Dada JB, Dare PA, Ayoade F, Olukanni AT. Resourcefulness of propylprodigiosin isolated from Brevundimonas olei strain RUN-D1. AMB Express 2023; 13:71. [PMID: 37422847 DOI: 10.1186/s13568-023-01579-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/11/2023] Open
Abstract
A novel red-pigmented bacterium was isolated from a water sample collected at Osun River, Ede. Morphological and 16 S rRNA gene sequencing revealed that the bacterium is a strain of Brevundimonas olei, while its red pigment was identified using UV-visible, FTIR and GCMS as a derivative of propylprodigiosin. The maximum absorbance of 534 nm, the FTIR's 1344 cm- 1 peak of prodigiosin's methoxyl C-O interaction, and the molecular ions from GCMS confirmed the pigment's identity. The pigments production was temperature-sensitive (25 °C), lost at > 28 °C, and in the presence of urea and humus. In addition, the pigment turned pink in the presence of hydrocarbons, while its red colour was retained with KCN and Fe2SO4, and enhanced by methylparaben. Furthermore, the pigment is stable in high temperature, salt, and acidic conditions, but changed to yellow in alkaline solution. The pigment, identified as propylprodigiosin (m/z 297), demonstrated broad-spectrum antibacterial activities against clinically important strains of Staphylococcus aureus (ATCC25923), Pseudomonas aeruginosa (ATCC9077), Bacillus cereus (ATCC10876), Salmonella typhi (ATCC13311), and Escherichia coli (DSM10974). The ethanol extract has the highest zones of inhibition of 29 ± 3.0, 26 ± 1.2, 22 ± 3.0, 22 ± 1.5, and 20 ± 2.0 mm, respectively. Furthermore, the acetone pigments interacted with cellulose and glucose such that increasing glucose concentrations showed linearity at 425 nm. Finally, the fastness of the pigments to fabrics was excellent, with percentage fadedness of 0 and - 43% light and washing tests, respectively, in the presence of Fe2SO4 as the mordant. The antibacterial nature of prodigiosin solutions and their good textile fastness to fabrics could be essential in manufacturing antiseptic materials such as bandages, hospital clothing and agricultural applications such as tubers preservation.Key points.
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Affiliation(s)
- Olumide D Olukanni
- Department of Biochemistry, Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria.
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria.
| | - Temitope Abiola
- Department of Biochemistry, Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria
| | - Jonathan B Dada
- Department of Biochemistry, Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria
| | - Peter A Dare
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria
- Department of Biological Sciences, Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria
| | - Femi Ayoade
- Department of Biological Sciences, Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria
| | - Adedayo T Olukanni
- Department of Biochemistry, Redeemer's University, PMB 230 Ede, Ede, Osun, Nigeria
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4
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Guevara YAS, Santos MHC, Gomes FIR, Mesquita FP, Souza PFN. A historical, economic, and technical-scientific approach to the current crisis in the development of antibacterial drugs: Promising role of antibacterial peptides in this scenario. Microb Pathog 2023; 179:106108. [PMID: 37044203 DOI: 10.1016/j.micpath.2023.106108] [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: 03/10/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
The emergence of antibiotic resistance (AMR) is a global public health problem. According to estimates, drug-resistant bacteria infect 2 million patients and perish 23,000 annually. To overcome this problem, antimicrobial peptides became a potential solution based on a new mechanism of action against bacteria. This article addresses the phenomenon of antibacterial resistance in most of its nuances, responding to historical, technical-scientific, and economic aspects. Likewise, it explores new therapeutic approaches to combat multi-resistant pathogens, specifically concerning antibacterial peptides, as a potential therapeutic tool to mitigate the current crisis of antibacterial drugs. It is expected that, with technological advances, especially with the advent and adoption of artificial intelligence, there will be an increase in diversified synthetic peptide production, which can face the challenges that we have in terms of antibacterial drugs.
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Affiliation(s)
- Yeimer A S Guevara
- Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Maria H C Santos
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Francisco I R Gomes
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Felipe P Mesquita
- Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Pedro F N Souza
- Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, Ceará, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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Heterologous Expression Reveals Ancient Properties of Tei3—A VanS Ortholog from the Teicoplanin Producer Actinoplanes teichomyceticus. Int J Mol Sci 2022; 23:ijms232415713. [PMID: 36555354 PMCID: PMC9779433 DOI: 10.3390/ijms232415713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Glycopeptide antibiotics (GPAs) are among the most clinically successful antimicrobials. GPAs inhibit cell-wall biosynthesis in Gram-positive bacteria via binding to lipid II. Natural GPAs are produced by various actinobacteria. Being themselves Gram-positives, the GPA producers evolved sophisticated mechanisms of self-resistance to avoid suicide during antibiotic production. These self-resistance genes are considered the primary source of GPA resistance genes actually spreading among pathogenic enterococci and staphylococci. The GPA-resistance mechanism in Actinoplanes teichomyceticus—the producer of the last-resort-drug teicoplanin—has been intensively studied in recent years, posing relevant questions about the role of Tei3 sensor histidine kinase. In the current work, the molecular properties of Tei3 were investigated. The setup of a GPA-responsive assay system in the model Streptomyces coelicolor allowed us to demonstrate that Tei3 functions as a non-inducible kinase, conferring high levels of GPA resistance in A. teichomyceticus. The expression of different truncated versions of tei3 in S. coelicolor indicated that both the transmembrane helices of Tei3 are crucial for proper functioning. Finally, a hybrid gene was constructed, coding for a chimera protein combining the Tei3 sensor domain with the kinase domain of VanS, with the latter being the inducible Tei3 ortholog from S. coelicolor. Surprisingly, such a chimera did not respond to teicoplanin, but indeed to the related GPA A40926. Coupling these experimental results with a further in silico analysis, a novel scenario on GPA-resistance and biosynthetic genes co-evolution in A. teichomyceticus was hereby proposed.
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Wu L, Zhang Q, Deng Z, Yu Y. From solo to duet, intersections of natural product assembly with self-resistance. Nat Prod Rep 2022; 39:919-925. [PMID: 34989738 DOI: 10.1039/d1np00064k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to 2021Self-resistance mechanisms adopted by natural product producers have long been recognized and studied as a standalone system separated from the assembly machinery. However, as more examples of self-resistance have been characterized in detail, it has been revealed that self-resistance could associate with the assembly machinery to fulfill the task of biosynthesis. This review summarizes different self-resistance mechanisms showing a common feature: intersection with natural product assembly. Furthermore, their possible evolutionary origin and synthetic biology applications are discussed.
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Affiliation(s)
- Linrui Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Qian Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
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7
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Traykovska M, Popova KB, Penchovsky R. Targeting glmS Ribozyme with Chimeric Antisense Oligonucleotides for Antibacterial Drug Development. ACS Synth Biol 2021; 10:3167-3176. [PMID: 34734706 DOI: 10.1021/acssynbio.1c00443] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Due to the steady rise of multidrug-resistant pathogenic bacteria worldwide, it is critical to develop novel antibacterial drugs. This article presents chimeric antisense oligonucleotides that inhibit the bacterial growth of Staphylococcus aureus, one of the most frequent causes of hospital-acquired infections. The chimeric antisense oligonucleotides have a combination of first- and second-generation chemical modification. To deliver the antisense oligonucleotides into a cell, we apply a cell-penetrating oligopeptide attached to them. We have performed complete bioinformatics analyses of the glmS ribozyme present in S. aureus and its essential role in the biochemical pathway of glucosamine-6-phosphate synthesis. Besides, we have analyzed the bacteria for alternative metabolic pathways, such as the nagA gene. The first antisense oligonucleotide explicitly targets the glmS riboswitch, while the second explicitly targets the nagA mRNA. We have evaluated that combined, the antisense oligonucleotides block the synthesis of glucosamine-6-phosphate entirely and inhibit the bacterial growth of S. aureus. However, the glmS riboswitch targeting the antisense oligonucleotide is sufficient to inhibit the growth of S. aureus with a MIC80 of 5 μg/mL. The glmS ribozyme is a very suitable target for antibacterial drug development with antisense oligonucleotides.
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Affiliation(s)
- Martina Traykovska
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Boulevard, 1164 Sofia, Bulgaria
| | - Katya B. Popova
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Boulevard, 1164 Sofia, Bulgaria
| | - Robert Penchovsky
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8 Dragan Tzankov Boulevard, 1164 Sofia, Bulgaria
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8
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Forneris CC, Nguy AKL, Seyedsayamdost MR. Mapping and Exploiting the Promiscuity of OxyB toward the Biocatalytic Production of Vancomycin Aglycone Variants. ACS Catal 2020; 10:9287-9298. [PMID: 34422446 PMCID: PMC8378672 DOI: 10.1021/acscatal.0c01719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vancomycin is one of the most important clinical antibiotics in the fight against infectious disease. Its biological activity relies on three aromatic cross-links, which create a cup-shaped topology and allow tight binding to nascent peptidoglycan chains. The cytochrome P450 enzymes OxyB, OxyA, and OxyC have been shown to introduce these synthetically challenging aromatic linkages. The ability to utilize the P450 enzymes in a chemo-enzymatic scheme to generate vancomycin derivatives is appealing but requires a thorough understanding of their reactivities and mechanisms. Herein, we systematically explore the scope of OxyB biocatalysis and report installation of diverse diaryl ether and biaryl cross-links with varying macrocycle sizes and compositions, when the enzyme is presented with modified vancomycin precursor peptides. The structures of the resulting products were determined using one-dimensional/two-dimensional nuclear magnetic resonance spectroscopy, high-resolution mass spectrometry (HR-MS), tandem HR-MS, and isotopic labeling, as well as ultraviolet-visible light absorption and fluorescence emission spectroscopies. An exploration of the biological activities of these alternative OxyB products surprisingly revealed antifungal properties. Taking advantage of the promiscuity of OxyB, we chemo-enzymatically generated a vancomycin aglycone variant containing an expanded macrocycle. Mechanistic implications for OxyB and future directions for creating vancomycin analogue libraries are discussed.
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Affiliation(s)
- Clarissa C Forneris
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Andy K L Nguy
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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9
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Marschall E, Cryle MJ, Tailhades J. Biological, chemical, and biochemical strategies for modifying glycopeptide antibiotics. J Biol Chem 2019; 294:18769-18783. [PMID: 31672921 DOI: 10.1074/jbc.rev119.006349] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the discovery of vancomycin in the 1950s, the glycopeptide antibiotics (GPAs) have been of great interest to the scientific community. These nonribosomally biosynthesized peptides are highly cross-linked, often glycosylated, and inhibit bacterial cell wall assembly by interfering with peptidoglycan synthesis. Interest in glycopeptide antibiotics covers many scientific disciplines, due to their challenging total syntheses, complex biosynthesis pathways, mechanism of action, and high potency. After intense efforts, early enthusiasm has given way to a recognition of the challenges in chemically synthesizing GPAs and of the effort needed to study and modify GPA-producing strains to prepare new GPAs to address the increasing threat of microbial antibiotic resistance. Although the preparation of GPAs, either by modifying the pendant groups such as saccharides or by functionalizing the N- or C-terminal moieties, is readily achievable, the peptide core of these molecules-the GPA aglycone-remains highly challenging to modify. This review aims to present a summary of the results of GPA modification obtained with the three major approaches developed to date: in vivo strain manipulation, total chemical synthesis, and chemoenzymatic synthesis methods.
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Affiliation(s)
- Edward Marschall
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.
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10
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Hashempour-Baltork F, Hosseini H, Shojaee-Aliabadi S, Torbati M, Alizadeh AM, Alizadeh M. Drug Resistance and the Prevention Strategies in Food Borne Bacteria: An Update Review. Adv Pharm Bull 2019; 9:335-347. [PMID: 31592430 PMCID: PMC6773942 DOI: 10.15171/apb.2019.041] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 01/10/2023] Open
Abstract
Antibiotic therapy is among the most important treatments against infectious diseases and has tremendously improved effects on public health. Nowadays, development in using this treatment has led us to the emergence and enhancement of drug-resistant pathogens which can result in some problems including treatment failure, increased mortality as well as treatment costs, reduced infection control efficiency, and spread of resistant pathogens from hospital to community. Therefore, many researches have tried to find new alternative approaches to control and prevent this problem. This study, has been revealed some possible and effective approaches such as using farming practice, natural antibiotics, nano-antibiotics, lactic acid bacteria, bacteriocin, cyclopeptid, bacteriophage, synthetic biology and predatory bacteria as alternatives for traditional antibiotics to prevent or reduce the emergence of drug resistant bacteria.
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Affiliation(s)
- Fataneh Hashempour-Baltork
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hedayat Hosseini
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Food Safety Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeedeh Shojaee-Aliabadi
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadali Torbati
- Department of Food Science and Technology, Faculty of Nutrition, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Adel Mirza Alizadeh
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Matin Alizadeh
- Department of Clinical Sciences (Surgery), Faculty of Specialized Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
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11
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Lipoglycopeptide Antibiotics: Reliable Fighters Against Gram-Positive Pathogens. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2018. [DOI: 10.5812/archcid.59526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Guo H. Design, Synthesis, and Antibacterial Evaluation of Propylene-tethered 8-Methoxyl Ciprofloxacin-isatin Hybrids. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hua Guo
- School of Chemistry and Life Science; Anshan Normal University; Anshan 114007 Liaoning China
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13
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Engineering modular intracellular protein sensor-actuator devices. Nat Commun 2018; 9:1881. [PMID: 29760420 PMCID: PMC5951936 DOI: 10.1038/s41467-018-03984-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Understanding and reshaping cellular behaviors with synthetic gene networks requires the ability to sense and respond to changes in the intracellular environment. Intracellular proteins are involved in almost all cellular processes, and thus can provide important information about changes in cellular conditions such as infections, mutations, or disease states. Here we report the design of a modular platform for intrabody-based protein sensing-actuation devices with transcriptional output triggered by detection of intracellular proteins in mammalian cells. We demonstrate reporter activation response (fluorescence, apoptotic gene) to proteins involved in hepatitis C virus (HCV) infection, human immunodeficiency virus (HIV) infection, and Huntington’s disease, and show sensor-based interference with HIV-1 downregulation of HLA-I in infected T cells. Our method provides a means to link varying cellular conditions with robust control of cellular behavior for scientific and therapeutic applications. Synthetic biology principles are often used to design circuits that tune gene expression in response to changes in intracellular environments. Here the authors design a modular platform for intracellular protein sensing devices with transcriptional output.
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14
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Hong H, Samborskyy M, Usachova K, Schnatz K, Leadlay PF. Sulfation and amidinohydrolysis in the biosynthesis of giant linear polyenes. Beilstein J Org Chem 2017; 13:2408-2415. [PMID: 29234468 PMCID: PMC5704753 DOI: 10.3762/bjoc.13.238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/13/2017] [Indexed: 12/24/2022] Open
Abstract
Clethramycin from Streptomyces malaysiensis DSM4137, and mediomycins (produced together with clethramycin from Streptomyces mediocidicus), are near-identical giant linear polyenes apparently constructed from, respectively, a 4-guanidinobutanoate or 4-aminobutanoate starter unit and 27 polyketide extender units, and bearing a specific O-sulfonate modification at the C-29 hydroxy group. We show here that mediomycins are actually biosynthesised not by use of a different starter unit but by direct late-stage deamidination of (desulfo)clethramycin. A gene (slf) encoding a candidate sulfotransferase has been located in both gene clusters. Deletion of this gene in DSM4137 led to accumulation of desulfoclethramycin only, instead of a mixture of desulfoclethramycin and clethramycin. The mediomycin gene cluster does not encode an amidinohydrolase, but when three candidate amidinohydrolase genes from elsewhere in the S. mediocidicus genome were individually expressed in Escherichia coli and assayed, only one of them (medi4948), located 670 kbp away from the mediomycin gene cluster on the chromosome, catalysed the removal of the amidino group from desulfoclethramycin. Subsequent cloning of medi4948 into DSM4137 caused mediomycins A and B to accumulate at the expense of clethramycin and desulfoclethramycin, respectively, a rare case where an essential biosynthetic gene is not co-located with other pathway genes. Clearly, both desulfoclethramycin and clethramycin are substrates for this amidinohydrolase. Also, purified recombinant sulfotransferase from DSM4137, in the presence of 3'-phosphoadenosine-5'-phosphosulfate as donor, efficiently converted mediomycin B to mediomycin A in vitro. Thus, in the final steps of mediomycin A biosynthesis deamidination and sulfotransfer can take place in either order.
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Affiliation(s)
- Hui Hong
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | | | - Katharina Schnatz
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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Abstract
The application of small molecules as catalysts for the diversification of natural product scaffolds is reviewed. Specifically, principles that relate to the selectivity challenges intrinsic to complex molecular scaffolds are summarized. The synthesis of analogues of natural products by this approach is then described as a quintessential "late-stage functionalization" exercise wherein natural products serve as the lead scaffolds. Given the historical application of enzymatic catalysts to the site-selective alteration of complex molecules, the focus of this Review is on the recent studies of nonenzymatic catalysts. Reactions involving hydroxyl group derivatization with a variety of electrophilic reagents are discussed. C-H bond functionalizations that lead to oxidations, aminations, and halogenations are also presented. Several examples of site-selective olefin functionalizations and C-C bond formations are also included. Numerous classes of natural products have been subjected to these studies of site-selective alteration including polyketides, glycopeptides, terpenoids, macrolides, alkaloids, carbohydrates, and others. What emerges is a platform for chemical remodeling of naturally occurring scaffolds that targets virtually all known chemical functionalities and microenvironments. However, challenges for the design of very broad classes of catalysts, with even broader selectivity demands (e.g., stereoselectivity, functional group selectivity, and site-selectivity) persist. Yet, a significant spectrum of powerful, catalytic alterations of complex natural products now exists such that expansion of scope seems inevitable. Several instances of biological activity assays of remodeled natural product derivatives are also presented. These reports may foreshadow further interdisciplinary impacts for catalytic remodeling of natural products, including contributions to SAR development, mode of action studies, and eventually medicinal chemistry.
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Affiliation(s)
- Christopher R. Shugrue
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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16
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Enabling techniques in the search for new antibiotics: Combinatorial biosynthesis of sugar-containing antibiotics. Biochem Pharmacol 2017; 134:56-73. [DOI: 10.1016/j.bcp.2016.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/24/2016] [Indexed: 12/12/2022]
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17
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Wright GD. Opportunities for natural products in 21 st century antibiotic discovery. Nat Prod Rep 2017; 34:694-701. [PMID: 28569300 DOI: 10.1039/c7np00019g] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Natural products and their derivatives are mainstays of our antibiotic drugs, but they are increasingly in peril. The combination of widespread multidrug resistance in once susceptible bacterial pathogens, disenchantment with natural products as sources of new drugs, lack of success using synthetic compounds and target-based discovery methods, along with shifting economic and regulatory issues, conspire to move investment in research and development away from the antibiotics arena. The result is a growing crisis in antibiotic drug discovery that threatens modern medicine. 21st century natural product research is perfectly positioned to fill the antibiotic discovery gap and bring new drug candidates to the clinic. Innovations in genomics and techniques to explore new sources of antimicrobial chemical matter are revealing new chemistry. Increasing appreciation of the value of narrow-spectrum drugs and re-examination of once discarded chemical scaffolds coupled with synthetic biology methods to generate new compounds and improve yields offer new strategies to revitalize once moribund natural product programs. The increasing awareness that the combination of antibiotics with adjuvants, non-antibiotic compounds that overcome resistance and enhance drug activity, can rescue older chemical scaffolds, and concepts such as blocking pathogen virulence present orthogonal strategies to traditional antibiotics. In all these areas, natural products offer chemical matter, shaped by natural selection, that is privileged in this therapeutic area. Natural product research is poised to regain prominence in delivering new drugs to solve the antibiotic crisis.
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Affiliation(s)
- Gerard D Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8N 4K1, Canada.
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18
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Brzozowski RS, Wuest WM. Twelve-membered macrolactones: privileged scaffolds for the development of new therapeutics. Chem Biol Drug Des 2017; 89:169-191. [PMID: 27153932 DOI: 10.1111/cbdd.12783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 12/15/2022]
Abstract
Natural products commonly produced as secondary metabolites of various plants and micro-organisms represent a diverse chemical space of compounds. The diversity of natural products makes them an attractive target for interrogation by both chemists and biologists alike. Indeed, the study of 12-membered macrolactones has already led to the discovery of lead drug compounds and new biological targets, which has motivated the development of diverted total synthetic routes to libraries of analogs. This review explores the discovery, biological characterization, and synthesis of several 12-membered macrolactones, exploiting examples that underscore their importance in the drug discovery field. It is our hope that this review will motivate further interest in this class of natural products, a group of molecules that we think merit the classification of 'privileged scaffolds' within the medicinal chemistry community, to further investigate and develop novel compounds with promising bioactivity.
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Affiliation(s)
| | - William M Wuest
- Department of Chemistry, Temple University, Philadelphia, PA, USA
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19
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Yim G, Wang W, Thaker MN, Tan S, Wright GD. How To Make a Glycopeptide: A Synthetic Biology Approach To Expand Antibiotic Chemical Diversity. ACS Infect Dis 2016; 2:642-650. [PMID: 27759388 DOI: 10.1021/acsinfecdis.6b00105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Modification of natural product backbones is a proven strategy for the development of clinically useful antibiotics. Such modifications have traditionally been achieved through medicinal chemistry strategies or via in vitro enzymatic activities. In an orthogonal approach, engineering of biosynthetic pathways using synthetic biology techniques can generate chemical diversity. Here we report the use of a minimal teicoplanin class glycopeptide antibiotic (GPA) scaffold expressed in a production-optimized Streptomyces coelicolor strain to expand GPA chemical diversity. Thirteen scaffold-modifying enzymes from 7 GPA biosynthetic gene clusters in different combinations were introduced into S. coelicolor, enabling us to explore the criteria for in-cell GPA modification. These include identifying specific isozymes that tolerate the unnatural GPA scaffold and modifications that prevent or allow further elaboration by other enzymes. Overall, 15 molecules were detected, 9 of which have not been reported previously. Some of these compounds showed activity against GPA-resistant bacteria. This system allows us to observe the complex interplay between substrates and both non-native and native tailoring enzymes in a cell-based system and establishes rules for GPA synthetic biology and subsequent expansion of GPA chemical diversity.
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Affiliation(s)
- Grace Yim
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Wenliang Wang
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Maulik N. Thaker
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Stephanie Tan
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Gerard D. Wright
- M. G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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20
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Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
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21
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Gray C, Thomas B, Upton R, Migas L, Eyers C, Barran P, Flitsch S. Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochim Biophys Acta Gen Subj 2016; 1860:1688-709. [DOI: 10.1016/j.bbagen.2016.02.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/21/2022]
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22
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Newman DJ, Cragg GM. Natural Products as Sources of New Drugs from 1981 to 2014. JOURNAL OF NATURAL PRODUCTS 2016; 79:629-61. [PMID: 26852623 DOI: 10.1021/acs.jnatprod.5b01055] [Citation(s) in RCA: 3679] [Impact Index Per Article: 459.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This contribution is a completely updated and expanded version of the four prior analogous reviews that were published in this journal in 1997, 2003, 2007, and 2012. In the case of all approved therapeutic agents, the time frame has been extended to cover the 34 years from January 1, 1981, to December 31, 2014, for all diseases worldwide, and from 1950 (earliest so far identified) to December 2014 for all approved antitumor drugs worldwide. As mentioned in the 2012 review, we have continued to utilize our secondary subdivision of a "natural product mimic", or "NM", to join the original primary divisions and the designation "natural product botanical", or "NB", to cover those botanical "defined mixtures" now recognized as drug entities by the U.S. FDA (and similar organizations). From the data presented in this review, the utilization of natural products and/or their novel structures, in order to discover and develop the final drug entity, is still alive and well. For example, in the area of cancer, over the time frame from around the 1940s to the end of 2014, of the 175 small molecules approved, 131, or 75%, are other than "S" (synthetic), with 85, or 49%, actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the anti-infective area being dependent on natural products and their structures. We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore it is considered that this area of natural product research should be expanded significantly.
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Affiliation(s)
- David J Newman
- NIH Special Volunteer, Wayne, Pennsylvania 19087, United States
| | - Gordon M Cragg
- NIH Special Volunteer, Bethesda, Maryland 20814, United States
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23
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Brieke C, Yim G, Peschke M, Wright GD, Cryle MJ. Catalytic promiscuity of glycopeptide N-methyltransferases enables bio-orthogonal labelling of biosynthetic intermediates. Chem Commun (Camb) 2016; 52:13679-13682. [DOI: 10.1039/c6cc06975d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Remarkable promiscuity of N-methyltransferases enables modulation of biological activity as well as bio-orthogonal labelling of glycopeptide antibiotics and biosynthetic intermediates.
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Affiliation(s)
- Clara Brieke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Grace Yim
- Department of Biochemistry and Biomedical Sciences
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Gerard D. Wright
- Department of Biochemistry and Biomedical Sciences
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada
| | - Max J. Cryle
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
- EMBL Australia
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24
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Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
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25
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Brieke C, Maier T, Schröter M, Cryle MJ. Design and synthesis of peptide inhibitor conjugates as probes of the Cytochrome P450s from glycopeptide antibiotic biosynthesis. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00332f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycopeptide antibiotics are important clinical antibiotics that are currently employed against serious Gram-positive bacterial infections.
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Affiliation(s)
- Clara Brieke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Theresa Maier
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Martin Schröter
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
| | - Max J. Cryle
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69120 Heidelberg
- Germany
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26
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Abstract
Synthetic biology (SB) is an emerging discipline, which is slowly reorienting the field of drug discovery. For thousands of years, living organisms such as plants were the major source of human medicines. The difficulty in resynthesizing natural products, however, often turned pharmaceutical industries away from this rich source for human medicine. More recently, progress on transformation through genetic manipulation of biosynthetic units in microorganisms has opened the possibility of in-depth exploration of the large chemical space of natural products derivatives. Success of SB in drug synthesis culminated with the bioproduction of artemisinin by microorganisms, a tour de force in protein and metabolic engineering. Today, synthetic cells are not only used as biofactories but also used as cell-based screening platforms for both target-based and phenotypic-based approaches. Engineered genetic circuits in synthetic cells are also used to decipher disease mechanisms or drug mechanism of actions and to study cell-cell communication within bacteria consortia. This review presents latest developments of SB in the field of drug discovery, including some challenging issues such as drug resistance and drug toxicity.
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Affiliation(s)
| | - Pablo Carbonell
- Faculty of Life Sciences, SYNBIOCHEM Centre, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Department of Experimental and Health Sciences (DCEXS), Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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27
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Reinvigorating natural product combinatorial biosynthesis with synthetic biology. Nat Chem Biol 2015; 11:649-59. [PMID: 26284672 DOI: 10.1038/nchembio.1893] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 12/24/2022]
Abstract
Natural products continue to play a pivotal role in drug-discovery efforts and in the understanding if human health. The ability to extend nature's chemistry through combinatorial biosynthesis--altering functional groups, regiochemistry and scaffold backbones through the manipulation of biosynthetic enzymes--offers unique opportunities to create natural product analogs. Incorporating emerging synthetic biology techniques has the potential to further accelerate the refinement of combinatorial biosynthesis as a robust platform for the diversification of natural chemical drug leads. Two decades after the field originated, we discuss the current limitations, the realities and the state of the art of combinatorial biosynthesis, including the engineering of substrate specificity of biosynthetic enzymes and the development of heterologous expression systems for biosynthetic pathways. We also propose a new perspective for the combinatorial biosynthesis of natural products that could reinvigorate drug discovery by using synthetic biology in combination with synthetic chemistry.
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28
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Harnessing natural product assembly lines: structure, promiscuity, and engineering. J Ind Microbiol Biotechnol 2015; 43:371-87. [PMID: 26527577 DOI: 10.1007/s10295-015-1704-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/18/2015] [Indexed: 10/22/2022]
Abstract
Many therapeutically relevant natural products are biosynthesized by the action of giant mega-enzyme assembly lines. By leveraging the specificity, promiscuity, and modularity of assembly lines, a variety of strategies has been developed that enables the biosynthesis of modified natural products. This review briefly summarizes recent structural advances related to natural product assembly lines, discusses chemical approaches to probing assembly line structures in the absence of traditional biophysical data, and surveys efforts that harness the inherent or engineered promiscuity of assembly lines for the synthesis of non-natural polyketides and non-ribosomal peptide analogues.
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29
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Yoganathan S, Miller SJ. Structure diversification of vancomycin through peptide-catalyzed, site-selective lipidation: a catalysis-based approach to combat glycopeptide-resistant pathogens. J Med Chem 2015; 58:2367-77. [PMID: 25671771 DOI: 10.1021/jm501872s] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of antibiotic-resistant infections highlights the need for novel antibiotic leads, perhaps with a broader spectrum of activity. Herein, we disclose a semisynthetic, catalytic approach for structure diversification of vancomycin. We have identified three unique peptide catalysts that exhibit site-selectivity for the lipidation of the aliphatic hydroxyls on vancomycin, generating three new derivatives 9a, 9b, and 9c. Incorporation of lipid chains into the vancomycin scaffold provides promising improvement of its bioactivity against vancomycin-resistant enterococci (Van A and Van B phenotypes of VRE). The MICs for 9a, 9b, and 9c against MRSA and VRE (Van B phenotype) range from 0.12 to 0.25 μg/mL. We have also performed a structure-activity relationship (SAR) study to investigate the effect of lipid chain length at the newly accessible G4-OH derivatization site.
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Affiliation(s)
- Sabesan Yoganathan
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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30
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Weber T, Charusanti P, Musiol-Kroll EM, Jiang X, Tong Y, Kim HU, Lee SY. Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends Biotechnol 2014; 33:15-26. [PMID: 25497361 DOI: 10.1016/j.tibtech.2014.10.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/21/2014] [Accepted: 10/31/2014] [Indexed: 12/15/2022]
Abstract
Actinomycetes are excellent sources for novel bioactive compounds, which serve as potential drug candidates for antibiotics development. While industrial efforts to find and develop novel antimicrobials have been severely reduced during the past two decades, the increasing threat of multidrug-resistant pathogens and the development of new technologies to find and produce such compounds have again attracted interest in this field. Based on improvements in whole-genome sequencing, novel methods have been developed to identify the secondary metabolite biosynthetic gene clusters by genome mining, to clone them, and to express them in heterologous hosts in much higher throughput than before. These technologies now enable metabolic engineering approaches to optimize production yields and to directly manipulate the pathways to generate modified products.
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Affiliation(s)
- Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Pep Charusanti
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ewa Maria Musiol-Kroll
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Xinglin Jiang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark
| | - Hyun Uk Kim
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
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31
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Binda E, Marinelli F, Marcone GL. Old and New Glycopeptide Antibiotics: Action and Resistance. Antibiotics (Basel) 2014; 3:572-94. [PMID: 27025757 PMCID: PMC4790382 DOI: 10.3390/antibiotics3040572] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/20/2014] [Accepted: 10/23/2014] [Indexed: 12/05/2022] Open
Abstract
Glycopeptides are considered antibiotics of last resort for the treatment of life-threatening infections caused by relevant Gram-positive human pathogens, such as Staphylococcus aureus, Enterococcus spp. and Clostridium difficile. The emergence of glycopeptide-resistant clinical isolates, first among enterococci and then in staphylococci, has prompted research for second generation glycopeptides and a flurry of activity aimed at understanding resistance mechanisms and their evolution. Glycopeptides are glycosylated non-ribosomal peptides produced by a diverse group of soil actinomycetes. They target Gram-positive bacteria by binding to the acyl-d-alanyl-d-alanine (d-Ala-d-Ala) terminus of the growing peptidoglycan on the outer surface of the cytoplasmatic membrane. Glycopeptide-resistant organisms avoid such a fate by replacing the d-Ala-d-Ala terminus with d-alanyl-d-lactate (d-Ala-d-Lac) or d-alanyl-d-serine (d-Ala-d-Ser), thus markedly reducing antibiotic affinity for the cellular target. Resistance has manifested itself in enterococci and staphylococci largely through the expression of genes (named van) encoding proteins that reprogram cell wall biosynthesis and, thus, evade the action of the antibiotic. These resistance mechanisms were most likely co-opted from the glycopeptide producing actinomycetes, which use them to avoid suicide during antibiotic production, rather than being orchestrated by pathogen bacteria upon continued treatment. van-like gene clusters, similar to those described in enterococci, were in fact identified in many glycopeptide-producing actinomycetes, such as Actinoplanes teichomyceticus, which produces teicoplanin, and Streptomyces toyocaensis, which produces the A47934 glycopeptide. In this paper, we describe the natural and semi-synthetic glycopeptide antibiotics currently used as last resort drugs for Gram-positive infections and compare the van gene-based strategies of glycopeptide resistance among the pathogens and the producing actinomycetes. Particular attention is given to the strategy of immunity recently described in Nonomuraea sp. ATCC 39727. Nonomuraea sp. ATCC 39727 is the producer of A40926, which is the natural precursor of the second generation semi-synthetic glycopeptide dalbavancin, very recently approved for acute bacterial skin and skin structure infections. A thorough understanding of glycopeptide immunity in this producing microorganism may be particularly relevant to predict and eventually control the evolution of resistance that might arise following introduction of dalbavancin and other second generation glycopeptides into clinics.
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Affiliation(s)
- Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
| | - Giorgia Letizia Marcone
- Department of Biotechnology and Life Sciences, University of Insubria, Varese 20100, Italy.
- The Protein Factory, Interuniversity Centre Politecnico di Milano, ICRM CNR Milano and University of Insubria, Milan 21100, Italy.
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32
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Antibiotic resistance-mediated isolation of scaffold-specific natural product producers. Nat Protoc 2014; 9:1469-79. [PMID: 24874813 DOI: 10.1038/nprot.2014.093] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
For over half a century, actinomycetes have served as the most promising source of novel antibacterial scaffolds. However, over the years, there has been a decline in the discovery of new antibiotics from actinomycetes. This is partly due to the use of standard screening methods and platforms that result in the re-discovery of the same molecules. Thus, according to current estimates, the discovery of a new antibacterial requires screening of tens to hundreds of thousands of bacterial strains. We have devised a resistance-based antibacterial discovery platform by harnessing the innate self-protection mechanism of antibiotic producers. This protocol provides a detailed method for isolation of scaffold-specific antibacterial producers by isolating strains in the presence of a selective antibiotic. As a specific example, we describe isolation of glycopeptide antibiotic (GPA) producers from soil actinomycetes, using vancomycin as the antibiotic resistance filter. However, the protocol can be adapted to isolate diverse producers from various sources producing different scaffolds, by selecting an appropriate antibiotic as a screening filter. The protocol provides a solution for two major bottlenecks that impede the new drug discovery pipeline: low hit frequency and re-discovery of known molecules. The entire protocol, from soil collection to identification of putative antibacterial producers, takes about 6 weeks to complete.
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33
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Wright GD. Something old, something new: revisiting natural products in antibiotic drug discovery. Can J Microbiol 2014; 60:147-54. [DOI: 10.1139/cjm-2014-0063] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antibiotic discovery is in crisis. Despite a growing need for new drugs resulting from the increasing number of multi-antibiotic-resistant pathogens, there have been only a handful of new antibiotics approved for clinical use in the past 2 decades. Faced with scientific, economic, and regulatory challenges, the pharmaceutical sector seems unable to respond to what has been called an “apocalyptic” threat. Natural products produced by bacteria and fungi are genetically encoded products of natural selection that have been the mainstay sources of the antibiotics in current clinical use. The pharmaceutical industry has largely abandoned these compounds in favor of large libraries of synthetic molecules because of difficulties in identifying new natural product antibiotics scaffolds. Advances in next-generation genome sequencing, bioinformatics, and analytical chemistry are combining to overcome barriers to natural products. Coupled with new strategies in antibiotic discovery, including inhibition of resistance, novel drug combinations, and new targets, natural products are poised for a renaissance to address what is a pressing health care crisis.
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Affiliation(s)
- Gerard D. Wright
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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Identifying producers of antibacterial compounds by screening for antibiotic resistance. Nat Biotechnol 2013; 31:922-7. [DOI: 10.1038/nbt.2685] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/07/2013] [Indexed: 12/28/2022]
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