1
|
Tian H, Holyoke CW, Fleming FF. Stereoselective Synthesis of ( E)- and ( Z)-Isocyanoalkenes. Org Lett 2022; 24:8657-8661. [PMID: 36399331 DOI: 10.1021/acs.orglett.2c03461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
(E)- and (Z)-isocyanoalkenes were selectively synthesized via the sequential cross coupling of vinyl iodides with formamide, followed by dehydration. The optimal catalyst, generated in situ from CuII and trans-N,N'-dimethyl-1,2-cyclohexanediamine, rapidly coupled (E)- or (Z)-vinyl iodides with formamide, which minimized the isomerization of the resultant vinyl formamide. The method efficiently provided a range of acyclic, carbocyclic, and heterocyclic isocyanoalkenes; the versatility is illustrated with the selective, stereodivergent syntheses of the diastereomeric isocyanoalkene antibiotics, B371 and E-B371.
Collapse
Affiliation(s)
- Huan Tian
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Caleb W Holyoke
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Fraser F Fleming
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
2
|
Flores ADR, Barber CC, Narayanamoorthy M, Gu D, Shen Y, Zhang W. Biosynthesis of Isonitrile- and Alkyne-Containing Natural Products. Annu Rev Chem Biomol Eng 2022; 13:1-24. [PMID: 35236086 PMCID: PMC9811556 DOI: 10.1146/annurev-chembioeng-092120-025140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.
Collapse
Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Colin C. Barber
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | | | - Di Gu
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA,Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
3
|
Verma S, Thapa S, Siddiqui N, Chakdar H. Cyanobacterial secondary metabolites towards improved commercial significance through multiomics approaches. World J Microbiol Biotechnol 2022; 38:100. [PMID: 35486205 DOI: 10.1007/s11274-022-03285-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are ubiquitous photosynthetic prokaryotes responsible for the oxygenation of the earth's reducing atmosphere. Apart from oxygen they are producers of a myriad of bioactive metabolites with diverse complex chemical structures and robust biological activities. These secondary metabolites are known to have a variety of medicinal and therapeutic applications ranging from anti-microbial, anti-viral, anti-inflammatory, anti-cancer, and immunomodulating properties. The present review discusses various aspects of secondary metabolites viz. biosynthesis, types and applications, which highlights the repertoire of bioactive constituents they harbor. Majority of these products have been produced from only a handful of genera. Moreover, with the onset of various OMICS approaches, cyanobacteria have become an attractive chassis for improved secondary metabolites production. Also the intervention of synthetic biology tools such as gene editing technologies and a variety of metabolomics and fluxomics approaches, used for engineering cyanobacteria, have significantly enhanced the production of secondary metabolites.
Collapse
Affiliation(s)
- Shaloo Verma
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.,Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India
| | - Nahid Siddiqui
- Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.
| |
Collapse
|
4
|
Zhukhovitskiy AV, Ratushnyy M, Ditzler RAJ. Advancing the Logic of Polymer Synthesis via Skeletal Rearrangements. Synlett 2022. [DOI: 10.1055/s-0041-1737456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractPolymers are ubiquitous materials that have driven technological innovation since the middle of the 20th century. As such, the logic that guides polymer synthesis merit considerable attention. Thus far, this logic has often been ‘forward-synthetic’, which constrains the accessible structures of polymer materials. In this article, we emphasize the benefits of ‘retrosynthetic’ logic and posit that the development of skeletal rearrangements of polymer backbones is central to the realization of this logic. To illustrate this point, we discuss two recent examples from our laboratory – Brook and Ireland–Claisen rearrangements of polymer backbones – and contextualize them in prior reports of sigmatropic rearrangements and skeletal rearrangements of polymers. We envision that further development of skeletal rearrangements of polymers will enable advances in not only the chemistry of such rearrangements and the logic of polymer synthesis, but also polymer re- and upcycling.
Collapse
|
5
|
Massarotti A, Brunelli F, Aprile S, Giustiniano M, Tron GC. Medicinal Chemistry of Isocyanides. Chem Rev 2021; 121:10742-10788. [PMID: 34197077 DOI: 10.1021/acs.chemrev.1c00143] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In eons of evolution, isocyanides carved out a niche in the ecological systems probably thanks to their metal coordinating properties. In 1859 the first isocyanide was synthesized by humans and in 1950 the first natural isocyanide was discovered. Now, at the beginning of XXI century, hundreds of isocyanides have been isolated both in prokaryotes and eukaryotes and thousands have been synthesized in the laboratory. For some of them their ecological role is known, and their potent biological activity as antibacterial, antifungal, antimalarial, antifouling, and antitumoral compounds has been described. Notwithstanding, the isocyanides have not gained a good reputation among medicinal chemists who have erroneously considered them either too reactive or metabolically unstable, and this has restricted their main use to technical applications as ligands in coordination chemistry. The aim of this review is therefore to show the richness in biological activity of the isocyanide-containing molecules, to support the idea of using the isocyanide functional group as an unconventional pharmacophore especially useful as a metal coordinating warhead. The unhidden hope is to convince the skeptical medicinal chemists of the isocyanide potential in many areas of drug discovery and considering them in the design of future drugs.
Collapse
Affiliation(s)
- Alberto Massarotti
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Francesca Brunelli
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Silvio Aprile
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Mariateresa Giustiniano
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli, Italy
| | - Gian Cesare Tron
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| |
Collapse
|
6
|
Al-Yousef HM, Amina M. Phytoconstituents and pharmacological activities of cyanobacterium Fischerella ambigua. ARAB J CHEM 2021. [DOI: 10.1016/j.arabjc.2021.103153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
7
|
Abstract
Covering: up to mid-2020 Terpenoids, also called isoprenoids, are the largest and most structurally diverse family of natural products. Found in all domains of life, there are over 80 000 known compounds. The majority of characterized terpenoids, which include some of the most well known, pharmaceutically relevant, and commercially valuable natural products, are produced by plants and fungi. Comparatively, terpenoids of bacterial origin are rare. This is counter-intuitive to the fact that recent microbial genomics revealed that almost all bacteria have the biosynthetic potential to create the C5 building blocks necessary for terpenoid biosynthesis. In this review, we catalogue terpenoids produced by bacteria. We collected 1062 natural products, consisting of both primary and secondary metabolites, and classified them into two major families and 55 distinct subfamilies. To highlight the structural and chemical space of bacterial terpenoids, we discuss their structures, biosynthesis, and biological activities. Although the bacterial terpenome is relatively small, it presents a fascinating dichotomy for future research. Similarities between bacterial and non-bacterial terpenoids and their biosynthetic pathways provides alternative model systems for detailed characterization while the abundance of novel skeletons, biosynthetic pathways, and bioactivies presents new opportunities for drug discovery, genome mining, and enzymology.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Tyler A Alsup
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Baofu Xu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Zining Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| |
Collapse
|
8
|
Hohlman RM, Sherman DH. Recent advances in hapalindole-type cyanobacterial alkaloids: biosynthesis, synthesis, and biological activity. Nat Prod Rep 2021; 38:1567-1588. [PMID: 34032254 DOI: 10.1039/d1np00007a] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 1984 up to the end of 2020Hapalindoles, fischerindoles, ambiguines and welwitindolinones are all members of a class of indole alkaloid natural products that have been isolated from the Stigonematales order of cyanobacteria. These compounds possess a polycyclic ring system, unique functional groups and various stereo- and regiochemical isomers. Since their initial isolation in 1984, they have been explored as potential therapeutics due to their wide variety of biological activities. Although numerous groups have pursued total syntheses of these densely functionalized structures, hapalindole biosynthesis has only recently been unveiled. Several groups have uncovered a wide range of novel enzymes that catalyze formation and tailoring of the hapalindole-type metabolites. In this article, we provide an overview of these natural products, their biological activities, highlight general synthetic routes, and provide an extensive review on the surprising biosynthetic processes leading to these structurally diverse metabolites.
Collapse
Affiliation(s)
- Robert M Hohlman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA. and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA. and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
9
|
Bunn BM, Xu M, Webb CM, Viswanathan R. Biocatalysts from cyanobacterial hapalindole pathway afford antivirulent isonitriles against MRSA. J Biosci 2021. [DOI: 10.1007/s12038-021-00156-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
10
|
Hohlman RM, Newmister SA, Sanders JN, Khatri Y, Li S, Keramati NR, Lowell AN, Houk KN, Sherman DH. Structural diversification of hapalindole and fischerindole natural products via cascade biocatalysis. ACS Catal 2021; 11:4670-4681. [PMID: 34354850 DOI: 10.1021/acscatal.0c05656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hapalindoles and related compounds (ambiguines, fischerindoles, welwitindolinones) are a diverse class of indole alkaloid natural products. They are typically isolated from the Stigonemataceae order of cyanobacteria and possess a broad scope of biological activities. Recently the biosynthetic pathway for assembly of these metabolites has been elucidated. In order to generate the core ring system, L-tryptophan is converted into the cis-indole isonitrile subunit before being prenylated with geranyl pyrophosphate at the C-3 position. A class of cyclases (Stig) catalyzes a three-step process including a Cope rearrangement, 6-exo-trig cyclization and electrophilic aromatic substitution to create a polycyclic core. Formation of the initial alkaloid is followed by diverse late-stage tailoring reactions mediated by additional biosynthetic enzymes to give rise to the wide array of structural variations observed in this compound class. Herein, we demonstrate the versatility and utility of the Fam prenyltransferase and Stig cyclases toward core structural diversification of this family of indole alkaloids. Through synthesis of cis-indole isonitrile subunit derivatives, and aided by protein engineering and computational analysis, we have employed cascade biocatalysis to generate a range of derivatives, and gained insights into the basis for substrate flexibility in this system.
Collapse
Affiliation(s)
| | | | - Jacob N. Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | | | | | | | | | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - David H. Sherman
- Department of Microbiology & Immunology, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, United States
| |
Collapse
|
11
|
Schraff S, Trampert J, Orthaber A, Pammer F. Electronic Properties and Solid-State Packing of Isocyanofulvenes and Their Gold(I) Chloride Complexes. Inorg Chem 2020; 59:17171-17183. [DOI: 10.1021/acs.inorgchem.0c02435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandra Schraff
- Institute of Organic Chemistry II and Advanced Materials, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jens Trampert
- Institute of Organic Chemistry II and Advanced Materials, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Andreas Orthaber
- Department of Chemistry−Ångström Laboratories, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Frank Pammer
- Institute of Organic Chemistry II and Advanced Materials, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| |
Collapse
|
12
|
Raji Reddy C, Sathish P, Mallesh K, Lakshmi Prapurna Y. Construction of Unique Polycyclic 3, 4‐Fused Indoles
via
Rhodium(III)‐Catalyzed Domino Annulations**. ChemistrySelect 2020. [DOI: 10.1002/slct.202002689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chada Raji Reddy
- Department of Organic Synthesis & Process Chemistry CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Hyderabad 500007 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201 002 India
| | - Puppala Sathish
- Department of Organic Synthesis & Process Chemistry CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Hyderabad 500007 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201 002 India
| | - Kathe Mallesh
- Department of Organic Synthesis & Process Chemistry CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Hyderabad 500007 India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad 201 002 India
| | - Y. Lakshmi Prapurna
- Department of Organic Synthesis & Process Chemistry CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Hyderabad 500007 India
| |
Collapse
|
13
|
Khatri Y, Hohlman RM, Mendoza J, Li S, Lowell AN, Asahara H, Sherman DH. Multicomponent Microscale Biosynthesis of Unnatural Cyanobacterial Indole Alkaloids. ACS Synth Biol 2020; 9:1349-1360. [PMID: 32302487 PMCID: PMC7323787 DOI: 10.1021/acssynbio.0c00038] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genome sequencing and bioinformatics tools have facilitated the identification and expression of an increasing number of cryptic biosynthetic gene clusters (BGCs). However, functional analysis of all components of a metabolic pathway to precisely determine biocatalytic properties remains time-consuming and labor intensive. One way to speed this process involves microscale cell-free protein synthesis (CFPS) for direct gene to biochemical function analysis, which has rarely been applied to study multicomponent enzymatic systems in specialized metabolism. We sought to establish an in vitro transcription/translation (TT)-assay to assess assembly of cyanobacterial-derived hapalindole-type natural products (cNPs) because of their diverse bioactivity profiles and complex structural diversity. Using a CFPS system including a plasmid bearing famD2 prenyltransferase from Fischerella ambigua UTEX 1903, we showed production of the central prenylated intermediate (3GC) in the presence of exogenous geranyl-pyrophosphate (GPP) and cis-indole isonitrile. Further addition of a plasmid bearing the famC1 Stig cyclase resulted in synthesis of both FamD2 and FamC1 enzymes, which was confirmed by proteomics analysis, and catalyzed assembly of 12-epi-hapalindole U. Further combinations of Stig cyclases (FamC1-C4) produced hapalindole U and hapalindole H, while FisC identified from Fischerella sp. SAG46.79 generated 12-epi-fischerindole U. The CFPS system was further employed to screen six unnatural halogenated cis-indole isonitrile substrates using FamC1 and FisC, and the reactions were scaled-up using chemoenzymatic synthesis and identified as 5- and 6-fluoro-12-epi-hapalindole U, and 5- and 6-fluoro-12-epi-fischerindole U, respectively. This approach represents an effective, high throughput strategy to determine the functional role of biosynthetic enzymes from diverse natural product BGCs.
Collapse
Affiliation(s)
| | | | | | | | | | - Haruichi Asahara
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
| | | |
Collapse
|
14
|
Li S, Newmister SA, Lowell AN, Zi J, Chappell CR, Yu F, Hohlman RM, Orjala J, Williams RM, Sherman DH. Control of Stereoselectivity in Diverse Hapalindole Metabolites is Mediated by Cofactor‐Induced Combinatorial Pairing of Stig Cyclases. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shasha Li
- Life Sciences InstituteDepartment of Medicinal ChemistryThe University of Michigan USA
| | | | - Andrew N. Lowell
- Life Science InstituteThe University of Michigan USA
- Department of ChemistryVirginia Tech Blacksburg VA 24061 USA
| | - Jiachen Zi
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Illinois at Chicago Chicago IL 60612 USA
| | - Callie R. Chappell
- Department of Molecular, Cellular & Developmental BiologyThe University of Michigan USA
| | - Fengan Yu
- Life Science InstituteThe University of Michigan USA
| | - Robert M. Hohlman
- Life Sciences InstituteDepartment of Medicinal ChemistryThe University of Michigan USA
| | - Jimmy Orjala
- Department of Pharmaceutical SciencesCollege of PharmacyUniversity of Illinois at Chicago Chicago IL 60612 USA
| | - Robert M. Williams
- Department of ChemistryColorado State University Fort Collins CO 80523 USA
- University of Colorado Cancer Center Aurora CO 80045 USA
| | - David H. Sherman
- Life Sciences InstituteDepartments of Medicinal Chemistry, Chemistry, Microbiology & ImmunologyThe University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109-2216n USA
| |
Collapse
|
15
|
Li S, Newmister SA, Lowell AN, Zi J, Chappell CR, Yu F, Hohlman RM, Orjala J, Williams RM, Sherman DH. Control of Stereoselectivity in Diverse Hapalindole Metabolites is Mediated by Cofactor-Induced Combinatorial Pairing of Stig Cyclases. Angew Chem Int Ed Engl 2020; 59:8166-8172. [PMID: 32052896 PMCID: PMC7274885 DOI: 10.1002/anie.201913686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Indexed: 11/07/2022]
Abstract
Stereospecific polycyclic core formation of hapalindoles and fischerindoles is controlled by Stig cyclases through a three-step cascade involving Cope rearrangement, 6-exo-trig cyclization, and a final electrophilic aromatic substitution. Reported here is a comprehensive study of all currently annotated Stig cyclases, revealing that these proteins can assemble into heteromeric complexes, induced by Ca2+ , to cooperatively control the stereochemistry of hapalindole natural products.
Collapse
Affiliation(s)
- Shasha Li
- Life Sciences Institute, Department of Medicinal Chemistry, The University of Michigan, USA
| | | | - Andrew N Lowell
- Life Science Institute, The University of Michigan, USA
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Jiachen Zi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Callie R Chappell
- Department of Molecular, Cellular & Developmental Biology, The University of Michigan, USA
| | - Fengan Yu
- Life Science Institute, The University of Michigan, USA
| | - Robert M Hohlman
- Life Sciences Institute, Department of Medicinal Chemistry, The University of Michigan, USA
| | - Jimmy Orjala
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
- University of Colorado Cancer Center, Aurora, CO, 80045, USA
| | - David H Sherman
- Life Sciences Institute, Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, The University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216n, USA
| |
Collapse
|
16
|
Sherikar MS, Devarajappa R, Prabhu KR. Weak Coordinating Carbonyl-Directed Rhodium(III)-Catalyzed C-H Activation at the C4-Position of Indole with Allyl Alcohols. J Org Chem 2020; 85:5516-5524. [PMID: 32192332 DOI: 10.1021/acs.joc.0c00277] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A weakly coordinating carbonyl-directed coupling of allyl alcohols at the C-4 position of indole derivatives under the C-H activation conditions catalyzed by Rh(III) is reported. This results in alkylation at the C-4 position of indole derivatives exclusively. The obtained product forms a tricyclic derivative under aldol reaction conditions, which can be a potential precursor for synthesizing a few alkaloid molecules such as ergot, hapalindole alkaloids, and related heterocyclic compounds.
Collapse
Affiliation(s)
| | - Ravi Devarajappa
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, Karnataka, India
| | - Kandikere Ramaiah Prabhu
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, Karnataka, India
| |
Collapse
|
17
|
Rudolf JD, Chang CY. Terpene synthases in disguise: enzymology, structure, and opportunities of non-canonical terpene synthases. Nat Prod Rep 2020; 37:425-463. [PMID: 31650156 PMCID: PMC7101268 DOI: 10.1039/c9np00051h] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to July 2019 Terpene synthases (TSs) are responsible for generating much of the structural diversity found in the superfamily of terpenoid natural products. These elegant enzymes mediate complex carbocation-based cyclization and rearrangement cascades with a variety of electron-rich linear and cyclic substrates. For decades, two main classes of TSs, divided by how they generate the reaction-triggering initial carbocation, have dominated the field of terpene enzymology. Recently, several novel and unconventional TSs that perform TS-like reactions but do not resemble canonical TSs in sequence or structure have been discovered. In this review, we identify 12 families of non-canonical TSs and examine their sequences, structures, functions, and proposed mechanisms. Nature provides a wide diversity of enzymes, including prenyltransferases, methyltransferases, P450s, and NAD+-dependent dehydrogenases, as well as completely new enzymes, that utilize distinctive reaction mechanisms for TS chemistry. These unique non-canonical TSs provide immense opportunities to understand how nature evolved different tools for terpene biosynthesis by structural and mechanistic characterization while affording new probes for the discovery of novel terpenoid natural products and gene clusters via genome mining. With every new discovery, the dualistic paradigm of TSs is contradicted and the field of terpene chemistry and enzymology continues to expand.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA.
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan, Republic of China
| |
Collapse
|
18
|
Rivilla I, Odriozola-Gimeno M, Aires A, Gimeno A, Jiménez-Barbero J, Torrent-Sucarrat M, Cortajarena AL, Cossío FP. Discovering Biomolecules with Huisgenase Activity: Designed Repeat Proteins as Biocatalysts for (3 + 2) Cycloadditions. J Am Chem Soc 2019; 142:762-776. [DOI: 10.1021/jacs.9b06823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Iván Rivilla
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Mikel Odriozola-Gimeno
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Antonio Aires
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
| | - Ana Gimeno
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Aitziber L. Cortajarena
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| |
Collapse
|
19
|
Jamieson CS, Ohashi M, Liu F, Tang Y, Houk KN. The expanding world of biosynthetic pericyclases: cooperation of experiment and theory for discovery. Nat Prod Rep 2019; 36:698-713. [PMID: 30311924 DOI: 10.1039/c8np00075a] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2018 Pericyclic reactions are a distinct class of reactions that have wide synthetic utility. Before the recent discoveries described in this review, enzyme-catalyzed pericyclic reactions were not widely known to be involved in biosynthesis. This situation is changing rapidly. We define the scope of pericyclic reactions, give a historical account of their discoveries as biosynthetic reactions, and provide evidence that there are many enzymes in nature that catalyze pericyclic reactions. These enzymes, the "pericyclases," are the subject of this review.
Collapse
Affiliation(s)
- Cooper S Jamieson
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
| | | | | | | | | |
Collapse
|
20
|
Knoot CJ, Khatri Y, Hohlman RM, Sherman DH, Pakrasi HB. Engineered Production of Hapalindole Alkaloids in the Cyanobacterium Synechococcus sp. UTEX 2973. ACS Synth Biol 2019; 8:1941-1951. [PMID: 31284716 DOI: 10.1021/acssynbio.9b00229] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria produce numerous valuable bioactive secondary metabolites (natural products) including alkaloids, isoprenoids, nonribosomal peptides, and polyketides. However, the genomic organization of the biosynthetic gene clusters, complex gene expression patterns, and low compound yields synthesized by the native producers currently limits access to the vast majority of these valuable molecules for detailed studies. Molecular cloning and expression of such clusters in heterotrophic hosts is often precarious owing to genetic and biochemical incompatibilities. Production of such biomolecules in photoautotrophic hosts analogous to the native producers is an attractive alternative that has been under-explored. Here, we describe engineering of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973 to produce key compounds of the hapalindole family of indole-isonitrile alkaloids. Engineering of the 42-kbp "fam" hapalindole pathway from the cyanobacterium Fischerella ambigua UTEX 1903 into S2973 was accomplished by rationally reconstructing six to seven core biosynthetic genes into synthetic operons. The resulting Synechococcus strains afforded controllable production of indole-isonitrile biosynthetic intermediates and hapalindoles H and 12-epi-hapalindole U at a titer of 0.75-3 mg/L. Exchanging genes encoding fam cyclase enzymes in the synthetic operons was employed to control the stereochemistry of the resulting product. Establishing a robust expression system provides a facile route to scalable levels of similar natural and new forms of bioactive hapalindole derivatives and its structural relatives (e.g., fischerindoles, welwitindolinones). Moreover, this versatile expression system represents a promising tool for exploring other functional characteristics of orphan gene products that mediate the remarkable biosynthesis of this important family of natural products.
Collapse
Affiliation(s)
- Cory J. Knoot
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| | - Yogan Khatri
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Robert M. Hohlman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Himadri B. Pakrasi
- Department of Biology, Washington University, St. Louis, Missouri 63130, United States
| |
Collapse
|
21
|
Awakawa T, Abe I. Molecular basis for the plasticity of aromatic prenyltransferases in hapalindole biosynthesis. Beilstein J Org Chem 2019; 15:1545-1551. [PMID: 31354873 PMCID: PMC6632223 DOI: 10.3762/bjoc.15.157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/02/2019] [Indexed: 12/25/2022] Open
Abstract
Aromatic prenyltransferases (PTases) are enzymes that catalyze Friedel–Crafts reactions between aromatic compounds and isoprenoid diphosphates. In hapalindole biosynthesis, the aromatic PTases AmbP1 and AmbP3 exhibit surprisingly plastic selectivities. AmbP1 not only transfers the geranyl group on the C-3 of cis-indolylvinyl isonitrile, but also on the C-2, which is supressed in the presence of Mg2+ ions. AmbP3 transfers the dimethylallyl group on C-2 of hapalindole U in the reverse manner, but on C-2 of its C-10 stereoisomer in the normal manner. This review highlights the molecular bases of the AmbP1 and AmbP3 functions, elucidated through their X-ray crystal structures. The knowledge presented here will contribute to the understanding of aromatic PTase reactions and will enhance their uses as biocatalysts.
Collapse
Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
22
|
Abstract
Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.
Collapse
|
23
|
Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
Collapse
Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
24
|
Chang M, Zhou Y, Wang H, Liu Z, Zhang Y, Feng Y. Crystal structure of the multifunctional SAM-dependent enzyme LepI provides insights into its catalytic mechanism. Biochem Biophys Res Commun 2019; 515:255-260. [PMID: 31101338 DOI: 10.1016/j.bbrc.2019.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations widely applied in the synthesis of multiple regioselective and stereoselective carbon-carbon bonds. LepI is a recently identified S-adenosyl-l-methionine (SAM)-dependent enzyme, which could catalyze dehydration, Diels-Alder reaction, and the retro-Claisen rearrangement reactions. However, the mechanism underlying these reactions by LepI remains elusive. Here we report the structure of LepI in complex with SAM as its co-factor, which adopts a typical class I methyltransferase fold. Docking studies are performed to investigate the binding modes of various substrates/products and provide insights into the catalytic mechanism of the multiple reactions catalyzed by LepI. Our study suggests that the dehydration reaction may start from the deprotonation of the hydroxyl group on the pyridone ring of the substrate by LepIH133, during which R295 and D296 play important roles in substrate binding and stabilizing the reaction intermediate. The stereoselective dehydration is accomplished through the trans-conformer of the leaving alcohol group which is trapped by nearby residues. The pericyclic reactions following dehydration are facilitated by the hydrophobic and hydrophilic interactions in the binding pocket. H133 and R295, two residues not conserved in other methyltransferases, might account for the unique activity of LepI among the SAM-dependent methyltransferase family. Together, this study provides important structural insights into the unique reactions catalyzed by LepI and will shed light on the knowledge of mechanisms of pericyclic reactions.
Collapse
Affiliation(s)
- Min Chang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, PR China
| | - Hao Wang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Zihe Liu
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yi Zhang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yue Feng
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China.
| |
Collapse
|
25
|
Tang X, Xue J, Yang Y, Ko TP, Chen CY, Dai L, Guo RT, Zhang Y, Chen CC. Structural insights into the calcium dependence of Stig cyclases. RSC Adv 2019; 9:13182-13185. [PMID: 35520811 PMCID: PMC9063808 DOI: 10.1039/c9ra00960d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/17/2019] [Indexed: 11/21/2022] Open
Abstract
The Stig cyclases from Stigonematalean cyanobacteria are classified as a novel type of calcium-dependent cyclases which catalyze an uncommon reaction cascade comprising Cope rearrangement, 6-exo-trig cyclization, and electrophilic aromatic substitution. Previously we found two calcium ions near the substrate-binding pocket. The calcium-coordinating residues are conserved in all Stig cyclases. In the present study, we use site-directed mutagenesis to investigate the role of calcium coordination. By individually mutating the coordinating residues in either of the Ca2+-binding sites to alanine, the enzyme activity is significantly reduced, suggesting that the presence of Ca2+ in both sites is essential for catalysis. Furthermore, the crystal structure of N137A, in which the Ca2+-binding N137 is replaced by Ala, shows significant local conformational changes, resulting in a squeezed substrate-binding pocket that makes substrate entry ineffective. In conclusion, calcium coordination is important in setting up the structural elements for catalysis. These results add to the fundamental understanding of the mechanism of action of the calcium-dependent Stig cyclases.
Collapse
Affiliation(s)
- Xueke Tang
- School of Life Sciences, University of Science and Technology of ChinaHefei 230026China,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin 300308China
| | - Jing Xue
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei UniversityWuhan430062China,College of Biotechnology, Tianjin University of Science and TechnologyTianjin 300457China
| | - Yunyun Yang
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijing 100084China
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia SinicaTaipei 11529Taiwan
| | - Chin-Yu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei UniversityWuhan430062China
| | - Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei UniversityWuhan430062China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei UniversityWuhan430062China,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin 300308China
| | - Yonghui Zhang
- School of Pharmaceutical Sciences, Tsinghua UniversityBeijing 100084China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei UniversityWuhan430062China
| |
Collapse
|
26
|
Sélem-Mojica N, Aguilar C, Gutiérrez-García K, Martínez-Guerrero CE, Barona-Gómez F. EvoMining reveals the origin and fate of natural product biosynthetic enzymes. Microb Genom 2019; 5. [PMID: 30946645 PMCID: PMC6939163 DOI: 10.1099/mgen.0.000260] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Natural products (NPs), or specialized metabolites, are important for medicine and agriculture alike, and for the fitness of the organisms that produce them. NP genome-mining aims at extracting biosynthetic information from the genomes of microbes presumed to produce these compounds. Typically, canonical enzyme sequences from known biosynthetic systems are identified after sequence similarity searches. Despite this being an efficient process, the likelihood of identifying truly novel systems by this approach is low. To overcome this limitation, we previously introduced EvoMining, a genome-mining approach that incorporates evolutionary principles. Here, we release and use our latest EvoMining version, which includes novel visualization features and customizable databases, to analyse 42 central metabolic enzyme families (EFs) conserved throughout Actinobacteria, Cyanobacteria, Pseudomonas and Archaea. We found that expansion-and-recruitment profiles of these 42 families are lineage specific, opening the metabolic space related to ‘shell’ enzymes. These enzymes, which have been overlooked, are EFs with orthologues present in most of the genomes of a taxonomic group, but not in all. As a case study of canonical shell enzymes, we characterized the expansion and recruitment of glutamate dehydrogenase and acetolactate synthase into scytonemin biosynthesis, and into other central metabolic pathways driving Archaea and Bacteria adaptive evolution. By defining the origin and fate of enzymes, EvoMining complements traditional genome-mining approaches as an unbiased strategy and opens the door to gaining insights into the evolution of NP biosynthesis. We anticipate that EvoMining will be broadly used for evolutionary studies, and for generating predictions of unprecedented chemical scaffolds and new antibiotics. This article contains data hosted by Microreact.
Collapse
Affiliation(s)
- Nelly Sélem-Mojica
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
| | - César Aguilar
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
| | | | - Christian E Martínez-Guerrero
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México.,Present address: Nuclear-Mitochondrial Interaction and Paleogenomics Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
| | - Fancisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, México
| |
Collapse
|
27
|
Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
| |
Collapse
|
28
|
Johnson RE, Ree H, Hartmann M, Lang L, Sawano S, Sarpong R. Total Synthesis of Pentacyclic (-)-Ambiguine P Using Sequential Indole Functionalizations. J Am Chem Soc 2019; 141:2233-2237. [PMID: 30702879 DOI: 10.1021/jacs.8b13388] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The first synthesis of a pentacyclic ambiguine (ambiguine P) is reported. The synthesis takes advantage of sequential alkylations of an indole core to rapidly construct the pentacyclic framework of the natural product. Key to the success of the synthesis was the use of a Nicholas reaction to alkylate at C2, crafting a fused seven-membered ring that is characteristic of the pentacyclic ambiguines, as well as the use of an amide-directed functionalization at C12 to set a requisite quaternary center. A versatile late-stage intermediate was prepared that may be applicable to the synthesis of the other pentacyclic ambiguines.
Collapse
Affiliation(s)
- Rebecca E Johnson
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Hwisoo Ree
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Marco Hartmann
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Laura Lang
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Shota Sawano
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Richmond Sarpong
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| |
Collapse
|
29
|
Chen C, Hu X, Tang X, Yang Y, Ko T, Gao J, Zheng Y, Huang J, Yu Z, Li L, Han S, Cai N, Zhang Y, Liu W, Guo R. The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chun‐Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
| | - Xiangying Hu
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Xueke Tang
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- School of Life SciencesUniversity of Science and Technology of China Anhui 230026 China
| | - Yunyun Yang
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Tzu‐Ping Ko
- Institute of Biological ChemistryAcademia Sinica Taipei 11529 Taiwan
| | - Jian Gao
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Yingying Zheng
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Jian‐Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
| | - Zhengsen Yu
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Liping Li
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Shuai Han
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Ningning Cai
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Yonghui Zhang
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Weidong Liu
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Rey‐Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| |
Collapse
|
30
|
Chen C, Hu X, Tang X, Yang Y, Ko T, Gao J, Zheng Y, Huang J, Yu Z, Li L, Han S, Cai N, Zhang Y, Liu W, Guo R. The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement. Angew Chem Int Ed Engl 2018; 57:15060-15064. [DOI: 10.1002/anie.201808231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/24/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Chun‐Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
| | - Xiangying Hu
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Xueke Tang
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
- School of Life SciencesUniversity of Science and Technology of China Anhui 230026 China
| | - Yunyun Yang
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Tzu‐Ping Ko
- Institute of Biological ChemistryAcademia Sinica Taipei 11529 Taiwan
| | - Jian Gao
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Yingying Zheng
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Jian‐Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
| | - Zhengsen Yu
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Liping Li
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Shuai Han
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Ningning Cai
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Yonghui Zhang
- School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua University Beijing 100084 China
| | - Weidong Liu
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Rey‐Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme EngineeringHubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei ProvinceHubei Key Laboratory of Industrial BiotechnologyCollege of Life SciencesHubei University Wuhan 430062 China
- Industrial Enzymes National Engineering LaboratoryTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| |
Collapse
|
31
|
Schraff S, Sun Y, Pammer F. Fulvenyl-Functionalized Polyisocyanides: Cross-Conjugated Electrochromic Polymers with Variable Optical and Electrochemical Properties. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00977] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sandra Schraff
- Ulm University, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| | - Yu Sun
- Technische
Universität
Kaiserslautern, Erwin-Schrödinger-Strasse 54, D-67663 Kaiserslautern, Germany
| | - Frank Pammer
- Ulm University, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
| |
Collapse
|
32
|
Abstract
Enzymes in biosynthetic pathways, especially in plant and microbial metabolism, generate structural and functional group complexity in small molecules by conversion of acyclic frameworks to cyclic scaffolds via short, efficient routes. The distinct chemical logic used by several distinct classes of cyclases, oxidative and non-oxidative, has recently been elucidated by genome mining, heterologous expression, and genetic and mechanistic analyses. These include enzymes performing pericyclic transformations, pyran synthases, tandem acting epoxygenases, and epoxide "hydrolases", as well as oxygenases and radical S-adenosylmethionine enzymes that involve rearrangements of substrate radicals under aerobic or anaerobic conditions.
Collapse
Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
| |
Collapse
|
33
|
Awakawa T, Mori T, Nakashima Y, Zhai R, Wong CP, Hillwig ML, Liu X, Abe I. Molecular Insight into the Mg 2+
-Dependent Allosteric Control of Indole Prenylation by Aromatic Prenyltransferase AmbP1. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yu Nakashima
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Rui Zhai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Chin Piow Wong
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Matthew L. Hillwig
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Xinyu Liu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| |
Collapse
|
34
|
Enantiospecific Total Syntheses of (+)-Hapalindole H and (−)-12-epi
-Hapalindole U. Chemistry 2018; 24:8980-8984. [DOI: 10.1002/chem.201800970] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 12/15/2022]
|
35
|
Awakawa T, Mori T, Nakashima Y, Zhai R, Wong CP, Hillwig ML, Liu X, Abe I. Molecular Insight into the Mg2+
-Dependent Allosteric Control of Indole Prenylation by Aromatic Prenyltransferase AmbP1. Angew Chem Int Ed Engl 2018; 57:6810-6813. [DOI: 10.1002/anie.201800855] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/29/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yu Nakashima
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Rui Zhai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Chin Piow Wong
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Matthew L. Hillwig
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Xinyu Liu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| |
Collapse
|
36
|
Newmister SA, Li S, Garcia-Borràs M, Sanders JN, Yang S, Lowell AN, Yu F, Smith JL, Williams RM, Houk KN, Sherman DH. Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis. Nat Chem Biol 2018. [PMID: 29531360 DOI: 10.1038/s41589-018-0003-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hapalindole alkaloids are a structurally diverse class of cyanobacterial natural products defined by their varied polycyclic ring systems and diverse biological activities. These complex metabolites are generated from a common biosynthetic intermediate by the Stig cyclases in three mechanistic steps: a rare Cope rearrangement, 6-exo-trig cyclization, and electrophilic aromatic substitution. Here we report the structure of HpiC1, a Stig cyclase that catalyzes the formation of 12-epi-hapalindole U in vitro. The 1.5-Å structure revealed a dimeric assembly with two calcium ions per monomer and with the active sites located at the distal ends of the protein dimer. Mutational analysis and computational methods uncovered key residues for an acid-catalyzed [3,3]-sigmatropic rearrangement, as well as specific determinants that control the position of terminal electrophilic aromatic substitution, leading to a switch from hapalindole to fischerindole alkaloids.
Collapse
Affiliation(s)
- Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Shasha Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrew N Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA. .,University of Colorado Cancer Center, Aurora, CO, USA.
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA. .,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA. .,Department of Chemistry, University of Michigan, Ann Arbor, MI, USA. .,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
37
|
Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
38
|
Wong CP, Awakawa T, Nakashima Y, Mori T, Zhu Q, Liu X, Abe I. Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3. Angew Chem Int Ed Engl 2017; 57:560-563. [DOI: 10.1002/anie.201710682] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Chin Piow Wong
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yu Nakashima
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Qin Zhu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Xinyu Liu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| |
Collapse
|
39
|
Miles ZD, Diethelm S, Pepper HP, Huang DM, George JH, Moore BS. A unifying paradigm for naphthoquinone-based meroterpenoid (bio)synthesis. Nat Chem 2017; 9:1235-1242. [PMID: 29168495 PMCID: PMC5960991 DOI: 10.1038/nchem.2829] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 06/15/2017] [Indexed: 12/14/2022]
Abstract
Bacterial meroterpenoids constitute an important class of natural products with diverse biological properties and therapeutic potential. The biosynthetic logic for their production is unknown and defies explanation via classical biochemical paradigms. A large subgroup of naphthoquinone-based meroterpenoids exhibits a substitution pattern of the polyketide-derived aromatic core that seemingly contradicts the established reactivity pattern of polyketide phenol nucleophiles and terpene diphosphate electrophiles. We report the discovery of a hitherto unprecedented enzyme-promoted α-hydroxyketone rearrangement catalysed by vanadium-dependent haloperoxidases to account for these discrepancies in the merochlorin and napyradiomycin class of meroterpenoid antibiotics, and we demonstrate that the α-hydroxyketone rearrangement is potentially a conserved biosynthetic reaction in this molecular class. The biosynthetic α-hydroxyketone rearrangement was applied in a concise total synthesis of naphthomevalin, a prominent member of the napyradiomycin meroterpenes, and sheds further light on the mechanism of this unifying enzymatic transformation.
Collapse
Affiliation(s)
- Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
| | - Stefan Diethelm
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
| | - Henry P. Pepper
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - David M. Huang
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jonathan H. George
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
40
|
SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis. Nature 2017; 549:502-506. [PMID: 28902839 PMCID: PMC5679075 DOI: 10.1038/nature23882] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/18/2017] [Indexed: 12/19/2022]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations to make multiple regioselective and stereoselective carbon-carbon bonds1. These reactions have been widely applied for the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centers2–6. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples, intramolecular Diels-Alder (IMDA) reaction7, Cope8 and Claisen rearrangements9, have been characterized. Here, we report the discovery of a S-adenosyl-L-methionine (SAM) dependent enzyme LepI that can catalyse stereoselective dehydration, bifurcating IMDA/hetero-DA (HDA) reactions via an ambimodal transition state, and a [3,3]-sigmatropic retro-Claisen rearrangement leading to the formation of dihydopyran core in the fungal natural product leporin10. Combined in vitro enzymatic characterization and computational studies provide evidence and mechanistic insight about how the O-methyltransferase-like protein LepI regulates the bifurcating biosynthetic reaction pathways (“direct” HDA and “byproduct recycle” IMDA/retro-Claisen reaction pathways) by utilizing SAM as the cofactor in order to converge to the desired biosynthetic end product. This work highlights that LepI is the first example of an enzyme catalysing a (SAM-dependent) retro-Claisen rearrangement. We suggest that more pericyclic biosynthetic enzymatic transformations are yet to be discovered in the intriguing enzyme toolboxes in Nature11, and propose an ever expanding role of the versatile cofactor SAM in enzyme catalysis.
Collapse
|
41
|
Jana S, Vroemans R, Dehaen W. Synthesis of Polycyclic Dihydroindoles by Selective Decomposition of Bis(1,2,3-triazoles) Mediated by Rhodium Catalysis. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700756] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sampad Jana
- Molecular Design and Synthesis; Department of Chemistry; KU Leuven; Celestijnenlaan 200F, B- 3001 Leuven Belgium
| | - Robby Vroemans
- Molecular Design and Synthesis; Department of Chemistry; KU Leuven; Celestijnenlaan 200F, B- 3001 Leuven Belgium
| | - Wim Dehaen
- Molecular Design and Synthesis; Department of Chemistry; KU Leuven; Celestijnenlaan 200F, B- 3001 Leuven Belgium
| |
Collapse
|
42
|
Chu H, Dai Q, Jiang Y, Cheng J. Synthesis of 2-Amino-3-hydroxy-3H-indoles via Palladium-Catalyzed One-Pot Reaction of Isonitriles, Oxygen, and N-Tosylhydrazones Derived from 2-Acylanilines. J Org Chem 2017; 82:8267-8272. [PMID: 28703584 DOI: 10.1021/acs.joc.7b01195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A cyanide-free one-pot procedure was developed to access 2-amino-3-hydroxy-3H-indoles, which involved: (1) in situ formation of ketenimines by the reaction of N'-(1-(2-aminophenyl)ethylidene)-p-tosylhydrazones with isonitriles; (2) the intramolecular nucleophilic attack of ketenimines by the amino in phenyl furnishing the ring closure leading to 2-aminoindoles; (3) the oxidation of 2-aminoindoles by O2 leading to 2-amino-3-hydroxy-3H-indoles. This strategy represents not only a key compliment to the sporadic synthetic methods toward 2-amino-3-hydroxy-3H-indoles but also progress in N-tosylhydrazone, isonitrile, and ketenimine chemistry.
Collapse
Affiliation(s)
- Haoke Chu
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical Engineering, Changzhou University , Changzhou 213164, P. R. China
| | - Qiang Dai
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical Engineering, Changzhou University , Changzhou 213164, P. R. China
| | - Yan Jiang
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical Engineering, Changzhou University , Changzhou 213164, P. R. China
| | - Jiang Cheng
- School of Petrochemical Engineering, Jiangsu Key Laboratory of Advanced Catalytic Materials & Technology, Jiangsu Province Key Laboratory of Fine Petrochemical Engineering, Changzhou University , Changzhou 213164, P. R. China
| |
Collapse
|
43
|
Zhu Q, Liu X. Discovery of a Calcium-Dependent Enzymatic Cascade for the Selective Assembly of Hapalindole-Type Alkaloids: On the Biosynthetic Origin of Hapalindole U. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201703932] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qin Zhu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Xinyu Liu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| |
Collapse
|
44
|
Zhu Q, Liu X. Discovery of a Calcium-Dependent Enzymatic Cascade for the Selective Assembly of Hapalindole-Type Alkaloids: On the Biosynthetic Origin of Hapalindole U. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703932] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qin Zhu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| | - Xinyu Liu
- Department of Chemistry; University of Pittsburgh; 219 Parkman Avenue Pittsburgh PA 15260 USA
| |
Collapse
|
45
|
Masschelein J, Jenner M, Challis GL. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Nat Prod Rep 2017. [PMID: 28650032 DOI: 10.1039/c7np00010c] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
Collapse
Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| |
Collapse
|
46
|
Kugel S, Baunach M, Baer P, Ishida-Ito M, Sundaram S, Xu Z, Groll M, Hertweck C. Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification. Nat Commun 2017. [PMID: 28643772 PMCID: PMC5481743 DOI: 10.1038/ncomms15804] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Terpenoid natural products comprise a wide range of molecular architectures that typically result from C–C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis. The crystal structure of XiaF with bound FADH2 (at 2.4 Å resolution) and phylogenetic analyses reveal that XiaF is, surprisingly, most closely related to xenobiotic-degrading enzymes. Biotransformation assays show that XiaF is a designated indole hydroxylase that can be used for the production of indigo and indirubin. We unveil a cryptic hydroxylation step that sets the basis for terpenoid cyclization and suggest that the cyclase has evolved from xenobiotics detoxification enzymes. The biosynthesis of xiamycin, an antimicrobial bacterial indolosesquiterpenoid, involves an unusual cyclization cascade. Here, the authors characterise the XiaF enzyme, which resembles xenobiont-degrading enzymes and is responsible for a hidden indole hydroxylation step that triggers the cyclization reaction.
Collapse
Affiliation(s)
- Susann Kugel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Martin Baunach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Baer
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Srividhya Sundaram
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zhongli Xu
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany.,Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany
| |
Collapse
|
47
|
Li S, Lowell AN, Newmister SA, Yu F, Williams RM, Sherman DH. Decoding cyclase-dependent assembly of hapalindole and fischerindole alkaloids. Nat Chem Biol 2017; 13:467-469. [PMID: 28288107 PMCID: PMC5391265 DOI: 10.1038/nchembio.2327] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 12/22/2016] [Indexed: 11/25/2022]
Abstract
The formation of C-C bonds in an enantioselective fashion to create complex polycyclic scaffolds in the hapalindole- and fischerindole- type alkaloids from Stigonematales cyanobacteria represents a compelling and urgent challenge in adapting microbial biosynthesis as a catalytic platform in drug development. Here we determine the biochemical basis for tri- and tetracyclic core formation in these secondary metabolites, involving a new class of cyclases that catalyze a complex cyclization cascade.
Collapse
Affiliation(s)
- Shasha Li
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew N Lowell
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengan Yu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert M Williams
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, USA
- University of Colorado Cancer Center, Aurora, Colorado, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology &Immunology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
48
|
Zhu Q, Liu X. Molecular and genetic basis for early stage structural diversifications in hapalindole-type alkaloid biogenesis. Chem Commun (Camb) 2017; 53:2826-2829. [DOI: 10.1039/c7cc00782e] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The genetic, molecular and biochemical basis for early stage structural diversification, post common intermediate 4, in the biosynthesis of hapalindole-type alkaloids is presented.
Collapse
Affiliation(s)
- Qin Zhu
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
| | - Xinyu Liu
- Department of Chemistry
- University of Pittsburgh
- Pittsburgh
- USA
| |
Collapse
|
49
|
Walton K, Berry JP. Indole Alkaloids of the Stigonematales (Cyanophyta): Chemical Diversity, Biosynthesis and Biological Activity. Mar Drugs 2016; 14:md14040073. [PMID: 27058546 PMCID: PMC4849077 DOI: 10.3390/md14040073] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 12/22/2022] Open
Abstract
The cyanobacteria are well recognized as producers of a wide array of bioactive metabolites including toxins, and potential drug candidates. However, a limited number of taxa are generally considered with respect to both of these aspects. That said, the order Stigonematales, although largely overlooked in this regard, has become increasingly recognized as a source of bioactive metabolites relevant to both human and environmental health. In particular, the hapalindoles and related indole alkaloids (i.e., ambiguines, fischerindoles, welwitindolinones) from the order, represent a diverse, and phylogenetically characteristic, class of secondary metabolites with biological activity suggestive of potential as both environmental toxins, and promising drug discovery leads. The present review gives an overview of the chemical diversity of biologically active metabolites from the Stigonematales—and particularly the so-called hapalindole-type alkaloids—including their biosynthetic origins, and their pharmacologically and toxicologically relevant bioactivities. Taken together, the current evidence suggests that these alkaloids, and the associated cyanobacterial taxa from the order, warrant future consideration as both potentially harmful (i.e., “toxic”) algae, and as promising leads for drug discovery.
Collapse
Affiliation(s)
- Katherine Walton
- Department of Chemistry and Biochemistry, Marine Science Program, Florida International University, 3000 NE 151st Street, North Miami, FL 33181, USA.
| | - John P Berry
- Department of Chemistry and Biochemistry, Marine Science Program, Florida International University, 3000 NE 151st Street, North Miami, FL 33181, USA.
| |
Collapse
|
50
|
Spallarossa M, Wang Q, Riva R, Zhu J. Synthesis of Vinyl Isocyanides and Development of a Convertible Isonitrile. Org Lett 2016; 18:1622-5. [PMID: 26981872 DOI: 10.1021/acs.orglett.6b00483] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction of isocyanomethylenetriphenylphosphorane, generated in situ from the corresponding phosphonium salt, with a diverse set of aldehydes afforded vinyl isocyanides in good to high yields. Excellent E-selectivity was observed for aliphatic aldehydes and 2,6-disubstituted aromatic aldehydes, whereas Z-olefins were formed predominantly with ortho-substituted aryl aldehydes. (Z)-1-Bromo-2-(2-isocyanovinyl)benzene (5l) was found to be a truly universal isonitrile since, after Ugi reaction, the resulting secondary amide unit (RNHCO-) is convertible under both acidic and basic conditions. The application of 5l in the synthesis of polyheterocycles is also illustrated.
Collapse
Affiliation(s)
- Martina Spallarossa
- Laboratory of Synthesis and Natural Products, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne , EPFL-SB-ISIC-LSPN, BCH 5304, 1015 Lausanne, Switzerland.,Department of Chemistry and Industrial Chemistry, University of Genova , Via Dodecaneso 31, 16146 Genova, Italy
| | - Qian Wang
- Laboratory of Synthesis and Natural Products, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne , EPFL-SB-ISIC-LSPN, BCH 5304, 1015 Lausanne, Switzerland
| | - Renata Riva
- Department of Chemistry and Industrial Chemistry, University of Genova , Via Dodecaneso 31, 16146 Genova, Italy
| | - Jieping Zhu
- Laboratory of Synthesis and Natural Products, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne , EPFL-SB-ISIC-LSPN, BCH 5304, 1015 Lausanne, Switzerland
| |
Collapse
|