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Zorn K, Back CR, Barringer R, Chadimová V, Manzo‐Ruiz M, Mbatha SZ, Mobarec J, Williams SE, van der Kamp MW, Race PR, Willis CL, Hayes MA. Interrogation of an Enzyme Library Reveals the Catalytic Plasticity of Naturally Evolved [4+2] Cyclases. Chembiochem 2023; 24:e202300382. [PMID: 37305956 PMCID: PMC10946715 DOI: 10.1002/cbic.202300382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
Stereoselective carbon-carbon bond forming reactions are quintessential transformations in organic synthesis. One example is the Diels-Alder reaction, a [4+2] cycloaddition between a conjugated diene and a dienophile to form cyclohexenes. The development of biocatalysts for this reaction is paramount for unlocking sustainable routes to a plethora of important molecules. To obtain a comprehensive understanding of naturally evolved [4+2] cyclases, and to identify hitherto uncharacterised biocatalysts for this reaction, we constructed a library comprising forty-five enzymes with reported or predicted [4+2] cycloaddition activity. Thirty-one library members were successfully produced in recombinant form. In vitro assays employing a synthetic substrate incorporating a diene and a dienophile revealed broad-ranging cycloaddition activity amongst these polypeptides. The hypothetical protein Cyc15 was found to catalyse an intramolecular cycloaddition to generate a novel spirotetronate. The crystal structure of this enzyme, along with docking studies, establishes the basis for stereoselectivity in Cyc15, as compared to other spirotetronate cyclases.
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Affiliation(s)
- Katja Zorn
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | - Rob Barringer
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | - Veronika Chadimová
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
| | | | | | - Juan‐Carlos Mobarec
- Mechanistic and Structural BiologyBiopharmaceuticals R&DAstraZenecaCambridgeCB21 6GHUK
| | | | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBristolBS8 1TDUK
| | | | - Martin A. Hayes
- Compound Synthesis and Management, Discovery SciencesBiopharmaceuticals R&DAstraZenecaPepparedsleden 1431 83MölndalSweden
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Igarashi Y. Development of a drug discovery approach from microbes with a special focus on isolation sources and taxonomy. J Antibiot (Tokyo) 2023:10.1038/s41429-023-00625-y. [PMID: 37188757 DOI: 10.1038/s41429-023-00625-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
After the successful discoveries of numerous antibiotics from microorganisms, frequent reisolation of known compounds becomes an obstacle in further development of new drugs from natural products. Exploration of biological sources that can provide novel scaffolds is thus an urgent matter in drug lead screening. As an alternative source to the conventionally used soil microorganisms, we selected endophytic actinomycetes, marine actinomycetes, and actinomycetes in tropical areas for investigation and found an array of new bioactive compounds. Furthermore, based on the analysis of the distribution pattern of biosynthetic gene clusters in bacteria together with available genomic data, we speculated that biosynthetic gene clusters for secondary metabolites are specific to each genus. Based on this assumption, we investigated actinomycetal and marine bacterial genera from which no compounds have been reported, which led to the discovery of a variety of skeletally novel bioactive compounds. These findings suggest that consideration of environmental factor and taxonomic position is critically effective in the selection of potential strains producing structurally unique compounds.
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Affiliation(s)
- Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.
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The biosynthetic pathway to tetromadurin (SF2487/A80577), a polyether tetronate antibiotic. PLoS One 2020; 15:e0239054. [PMID: 32925967 PMCID: PMC7489565 DOI: 10.1371/journal.pone.0239054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/30/2020] [Indexed: 12/03/2022] Open
Abstract
The type I polyketide SF2487/A80577 (herein referred to as tetromadurin) is a polyether tetronate ionophore antibiotic produced by the terrestrial Gram-positive bacterium Actinomadura verrucosospora. Tetromadurin is closely related to the polyether tetronates tetronasin (M139603) and tetronomycin, all of which are characterised by containing a tetronate, cyclohexane, tetrahydropyran, and at least one tetrahydrofuran ring. We have sequenced the genome of Actinomadura verrucosospora to identify the biosynthetic gene cluster responsible for tetromadurin biosynthesis (the mad gene cluster). Based on bioinformatic analysis of the 32 genes present within the cluster a plausible biosynthetic pathway for tetromadurin biosynthesis is proposed. Functional confirmation of the mad gene cluster is obtained by performing in-frame deletions in each of the genes mad10 and mad31, which encode putative cyclase enzymes responsible for cyclohexane and tetrahydropyran formation, respectively. Furthermore, the A. verrucosospora Δmad10 mutant produces a novel tetromadurin metabolite that according to mass spectrometry analysis is analogous to the recently characterised partially cyclised tetronasin intermediate lacking its cyclohexane and tetrahydropyran rings. Our results therefore elucidate the biosynthetic machinery of tetromadurin biosynthesis and lend support for a conserved mechanism of cyclohexane and tetrahydropyran biosynthesis across polyether tetronates.
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Secondary Metabolites of Endophytic Actinomycetes: Isolation, Synthesis, Biosynthesis, and Biological Activities. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 108 2019; 108:207-296. [DOI: 10.1007/978-3-030-01099-7_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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Abstract
The enzymology of 135 assembly lines containing primarily cis-acyltransferase modules is comprehensively analyzed, with greater attention paid to less common phenomena. Diverse online transformations, in which the substrate and/or product of the reaction is an acyl chain bound to an acyl carrier protein, are classified so that unusual reactions can be compared and underlying assembly-line logic can emerge. As a complement to the chemistry surrounding the loading, extension, and offloading of assembly lines that construct primarily polyketide products, structural aspects of the assembly-line machinery itself are considered. This review of assembly-line phenomena, covering the literature up to 2017, should thus be informative to the modular polyketide synthase novice and expert alike.
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Affiliation(s)
- Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
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Dinesh R, Srinivasan V, T E S, Anandaraj M, Srambikkal H. Endophytic actinobacteria: Diversity, secondary metabolism and mechanisms to unsilence biosynthetic gene clusters. Crit Rev Microbiol 2017; 43:546-566. [PMID: 28358596 DOI: 10.1080/1040841x.2016.1270895] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Endophytic actinobacteria, which reside in the inner tissues of host plants, are gaining serious attention due to their capacity to produce a plethora of secondary metabolites (e.g. antibiotics) possessing a wide variety of biological activity with diverse functions. This review encompasses the recent reports on endophytic actinobacterial species diversity, in planta habitats and mechanisms underlying their mode of entry into plants. Besides, their metabolic potential, novel bioactive compounds they produce and mechanisms to unravel their hidden metabolic repertoire by activation of cryptic or silent biosynthetic gene clusters (BGCs) for eliciting novel secondary metabolite production are discussed. The study also reviews the classical conservative techniques (chemical/biological/physical elicitation, co-culturing) as well as modern microbiology tools (e.g. next generation sequencing) that are being gainfully employed to uncover the vast hidden scaffolds for novel secondary metabolites produced by these endophytes, which would subsequently herald a revolution in drug engineering. The potential role of these endophytes in the agro-environment as promising biological candidates for inhibition of phytopathogens and the way forward to thoroughly exploit this unique microbial community by inducing expression of cryptic BGCs for encoding unseen products with novel therapeutic properties are also discussed.
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Affiliation(s)
- Raghavan Dinesh
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Sheeja T E
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
| | | | - Hamza Srambikkal
- a ICAR-Indian Institute of Spices Research , Kozhikode, Kerala , India
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Tetrodecamycin: An unusual and interesting tetronate antibiotic. Bioorg Med Chem 2016; 24:6269-6275. [DOI: 10.1016/j.bmc.2016.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/08/2016] [Accepted: 05/17/2016] [Indexed: 11/23/2022]
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Abstract
[4 + 2]-Cycloadditions are increasingly being recognized in the biosynthetic pathways of many structurally complex natural products. A relatively small collection of enzymes from these pathways have been demonstrated to increase rates of cyclization and impose stereochemical constraints on the reactions. While mechanistic investigation of these enzymes is just beginning, recent studies have provided new insights with implications for understanding their biosynthetic roles, mechanisms of catalysis, and evolutionary origin.
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Affiliation(s)
- Byung-Sun Jeon
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Shao-An Wang
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mark W Ruszczycky
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry and ‡Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
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