1
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Kumar V, Johnson BP, Mandal PS, Sheffield DR, Dimas DA, Das R, Maity S, Distefano MD, Singh S. The utility of Streptococcus mutans undecaprenol kinase for the chemoenzymatic synthesis of diverse non-natural isoprenoids. Bioorg Chem 2024; 151:107707. [PMID: 39128243 DOI: 10.1016/j.bioorg.2024.107707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/08/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
Isoprene chemoenzymatic cascades (ICCs) overcome the complexity of natural pathways by leveraging a streamlined two-enzyme cascade, facilitating efficient synthesis of C5-isoprene diphosphate precursors from readily available alcohol derivatives. Despite the documented promiscuity of enzymes in ICCs, exploration of their potential for accessing novel compounds remains limited, and existing methods require additional enzymes for generating longer-chain diphosphates. In this study, we present the utility of Streptococcus mutans undecaprenol kinase (SmUdpK) for the chemoenzymatic synthesis of diverse non-natural isoprenoids. Using a library of 50 synthetic alcohols, we demonstrate that SmUdpK's promiscuity extends to allylic chains as small as four carbons and benzylic alcohols with various substituents. Subsequently, SmUdpK is utilized in an ICC with isopentenyl phosphate kinase and aromatic prenyltransferase to generate multiple non-natural isoprenoids. This work provides evidence that, with proper optimization, SmUdpK can act as the first enzyme in these ICCs, enhancing access to both valuable and novel compounds.
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Affiliation(s)
- Vikas Kumar
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Bryce P Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Prashant S Mandal
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Daniel R Sheffield
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Dustin A Dimas
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States
| | - Riki Das
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States
| | - Sanjay Maity
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 1000, Norman, OK 73019, United States.
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2
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Miller ET, Tsodikov OV, Garneau-Tsodikova S. Structural insights into the diverse prenylating capabilities of DMATS prenyltransferases. Nat Prod Rep 2024; 41:113-147. [PMID: 37929638 DOI: 10.1039/d3np00036b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Covering: 2009 up to August 2023Prenyltransferases (PTs) are involved in the primary and the secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically relevant natural products (NPs). The continued biochemical and structural characterization of the soluble dimethylallyl tryptophan synthase (DMATS) PTs over the past two decades have revealed the significant promise that these enzymes hold as biocatalysts for the chemoenzymatic synthesis of novel drug leads. This is a comprehensive review of DMATSs describing the structure-function relationships that have shaped the mechanistic underpinnings of these enzymes, as well as the application of this knowledge to the engineering of DMATSs. We summarize the key findings and lessons learned from these studies over the past 14 years (2009-2023). In addition, we identify current gaps in our understanding of these fascinating enzymes.
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Affiliation(s)
- Evan T Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
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3
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Gardner ED, Johnson BP, Dimas DA, McClurg HE, Severance ZC, Burgett AW, Singh S. Unlocking New Prenylation Modes: Azaindoles as a New Substrate Class for Indole Prenyltransferases. ChemCatChem 2023; 15:e202300650. [PMID: 37954549 PMCID: PMC10634513 DOI: 10.1002/cctc.202300650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Indexed: 11/14/2023]
Abstract
Aza-substitution, the replacement of aromatic CH groups with nitrogen atoms, is an established medicinal chemistry strategy for increasing solubility, but current methods of accessing functionalized azaindoles are limited. In this work, indole-alkylating aromatic prenyltransferases (PTs) were explored as a strategy to directly functionalize azaindole-substituted analogs of natural products. For this, a series of aza-l-tryptophans (Aza-Trp) featuring N-substitution of every aromatic CH position of the indole ring and their corresponding cyclic Aza-l-Trp-l-proline dipeptides (Aza-CyWP), were synthesized as substrate mimetics for the indole-alkylating PTs FgaPT2, CdpNPT, and FtmPT1. We then demonstrated most of these substrate analogs were accepted by a PT, and the regioselectivity of each prenylation was heavily influenced by the position of the N-substitution. Remarkably, FgaPT2 was found to produce cationic N-prenylpyridinium products, representing not only a new substrate class for indole PTs but also a previously unobserved prenylation mode. The discovery that nitrogenous indole bioisosteres can be accepted by PTs thus provides access to previously unavailable chemical space in the search for bioactive indolediketopiperazine analogs.
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Affiliation(s)
- Eric D. Gardner
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Bryce P. Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Dustin A. Dimas
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Heather E. McClurg
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Zachary C. Severance
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Anthony W. Burgett
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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4
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Alexander AK, Elshahawi SI. Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization. Chembiochem 2023; 24:e202300372. [PMID: 37338668 PMCID: PMC10496146 DOI: 10.1002/cbic.202300372] [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: 05/18/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.
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Affiliation(s)
- Ashley K Alexander
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
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5
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Colombano A, Dalponte L, Dall'Angelo S, Clemente C, Idress M, Ghazal A, Houssen WE. Chemoenzymatic Late-Stage Modifications Enable Downstream Click-Mediated Fluorescent Tagging of Peptides. Angew Chem Int Ed Engl 2023; 62:e202215979. [PMID: 36815722 PMCID: PMC10946513 DOI: 10.1002/anie.202215979] [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: 10/30/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 02/24/2023]
Abstract
Aromatic prenyltransferases from cyanobactin biosynthetic pathways catalyse the chemoselective and regioselective intramolecular transfer of prenyl/geranyl groups from isoprene donors to an electron-rich position in these macrocyclic and linear peptides. These enzymes often demonstrate relaxed substrate specificity and are considered useful biocatalysts for structural diversification of peptides. Herein, we assess the isoprene donor specificity of the N1-tryptophan prenyltransferase AcyF from the anacyclamide A8P pathway using a library of 22 synthetic alkyl pyrophosphate analogues, of which many display reactive groups that are amenable to additional functionalization. We further used AcyF to introduce a reactive moiety into a tryptophan-containing cyclic peptide and subsequently used click chemistry to fluorescently label the enzymatically modified peptide. This chemoenzymatic strategy allows late-stage modification of peptides and is useful for many applications.
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Affiliation(s)
- Alessandro Colombano
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Luca Dalponte
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Sergio Dall'Angelo
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Claudia Clemente
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Mohannad Idress
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
- Abzena, Babraham Research CampusCambridgeUK
| | - Ahmad Ghazal
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Wael E. Houssen
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
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6
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Xuecheng C, Liang H, Yanpeng X, Yurong Z, Yue L, Yalan P, Zhong C, Jie Z, Zhijian Y, Shiqing H. Development of 2‐Alkyl‐5‐((phenylsulfonyl)oxy)‐1
H
‐indole‐3‐carboxylate Derivatives as Potential Anti‐Biofilm Agents. ChemistrySelect 2023. [DOI: 10.1002/slct.202204226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Chen Xuecheng
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University Nanjing 211816 China
| | - Hu Liang
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University Nanjing 211816 China
| | - Xiong Yanpeng
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University Nanjing 211816 China
- Department of Infectious Diseases and the Key Lab of Endogenous Infection Shenzhen Nanshan People's Hospital, the 6th Affiliated Hospital of Shenzhen University Medical School Shenzhen 518052 China
| | - Zhang Yurong
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University Nanjing 211816 China
| | - Luo Yue
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University Nanjing 211816 China
| | - Peng Yalan
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University Nanjing 211816 China
| | - Chen Zhong
- Department of Infectious Diseases and the Key Lab of Endogenous Infection Shenzhen Nanshan People's Hospital, the 6th Affiliated Hospital of Shenzhen University Medical School Shenzhen 518052 China
| | - Zhang Jie
- School of Animal Pharmaceutical Jiangsu Agri-animal Husbandry Vocational College Taizhou 225300 People's Republic of China
| | - Yu Zhijian
- Department of Infectious Diseases and the Key Lab of Endogenous Infection Shenzhen Nanshan People's Hospital, the 6th Affiliated Hospital of Shenzhen University Medical School Shenzhen 518052 China
| | - Han Shiqing
- College of Biotechnology and Pharmaceutical Engineering Nanjing Tech University Nanjing 211816 China
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7
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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8
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Hamdy SA, Kodama T, Nakashima Y, Han X, Morita H. Catalytic potential of a fungal indole prenyltransferase toward β-carbolines, harmine and harman, and their prenylation effects on antibacterial activity. J Biosci Bioeng 2022; 134:311-317. [PMID: 35931602 DOI: 10.1016/j.jbiosc.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
Abstract
The prenylation of compounds has attracted much attention, since it often adds bioactivity to non-prenylated compounds. We employed an enzyme assay with CdpNPT, an indole prenyltransferase from Aspergillus fumigatus with two naturally occurring β-carbolines, harmine (3) and harman (4) as prenyl acceptors, in the presence of dimethylallyl diphosphate (DMAPP) as the prenyl donor. The enzyme accepted these two prenyl acceptor substrates to produce 6-(3',3'-dimethylallyl)harmine (5) from 3 and 9-(3',3'-dimethylallyl)harman (6) and 6-(3',3'-dimethylallyl)harman (7) from 4. The X-ray crystal structure analysis of the CdpNPT (38-440) truncated mutant complexed with 4, and docking simulation studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant, suggested that CdpNPT could employ the two-step prenylation mechanism to produce 7, while the enzyme produced 6 with either one- or two-step prenylation mechanisms. Furthermore, the antibacterial assays revealed that the 3',3'-dimethylallylation of 3 and 4, as well as harmol (1), at C-6 enhanced the activities against Staphylococcus aureus and Bacillus subtilis.
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Affiliation(s)
- Sherif Ahmed Hamdy
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt; Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Takeshi Kodama
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Yu Nakashima
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Xiaojie Han
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Hiroyuki Morita
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan.
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9
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Enzymatic formation of a prenyl β-carboline by a fungal indole prenyltransferase. J Nat Med 2022; 76:873-879. [PMID: 35767141 DOI: 10.1007/s11418-022-01635-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
Abstract
CdpNPT from Aspergillus fumigatus is a fungal indole prenyltransferase (IPT) with remarkable substrate promiscuity to generate prenylated compounds. Our first investigation of the catalytic potential of CdpNPT against a β-carboline, harmol (1), revealed that the enzyme also accepts 1 as the prenyl acceptor with dimethylallyl diphosphate (DMAPP) as the prenyl donor and selectively prenylates the C-6 position of 1 by the "regular-type" dimethylallylation to produce 6-(3-dimethylallyl)harmol (2). Furthermore, our X-ray crystal structure analysis of the C-His6-tagged CdpNPT (38-440) truncated mutant complexed with 1 and docking studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant suggested that CdpNPT could employ the two-step prenylation system to produce 2.
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10
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Barnawi G, Noden M, Goodyear J, Marlyn J, Schneider O, Beriashvili D, Schulz S, Moreira R, Palmer M, Taylor SD. Discovery of Highly Active Derivatives of Daptomycin by Assessing the Effect of Amino Acid Substitutions at Positions 8 and 11 on a Daptomycin Analogue. ACS Infect Dis 2022; 8:778-789. [PMID: 35317552 DOI: 10.1021/acsinfecdis.1c00483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Daptomycin is an important antibiotic used for treating serious infections caused by Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci. Establishing structure-activity relationships of daptomycin is important for developing new daptomycin-based antibiotics with expanded clinical applications and for tackling the ever-increasing problem of antimicrobial resistance. Toward this end, Dap-K6-E12-W13, an active analogue of daptomycin in which the uncommon amino acids in daptomycin are replaced with their common counterparts, was used as a model system for studying the effect of amino acid variation at positions 8 and 11 on in vitro biological activity against a model organism, Bacillus subtilis, and calcium-dependent insertion into model membranes. None of the new peptides were more active than Dap-K6-E12-W13; however, substitution at positions 8 and/or 11 with cationic residues resulted in little or no loss of activity, and some of these analogues were able to insert into model membranes at lower calcium ion concentrations than the parent peptide. Incorporation of these cationic residues into positions 8 and/or 11 of daptomycin itself yielded some derivatives that exhibited lower minimum inhibitory concentrations than daptomycin against B. subtilis 1046 as well as comparable and sometimes superior activity against clinical isolates of MRSA.
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Affiliation(s)
- Ghufran Barnawi
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Michael Noden
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Jeremy Goodyear
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Julian Marlyn
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Olivia Schneider
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - David Beriashvili
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Sarah Schulz
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Michael Palmer
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Scott D. Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
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11
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Mupparapu N, Brewster L, Ostrom KF, Elshahawi SI. Late-Stage Chemoenzymatic Installation of Hydroxy-Bearing Allyl Moiety on the Indole Ring of Tryptophan-Containing Peptides. Chemistry 2022; 28:e202104614. [PMID: 35178791 PMCID: PMC9314954 DOI: 10.1002/chem.202104614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Indexed: 01/08/2023]
Abstract
The late‐stage functionalization of indole‐ and tryptophan‐containing compounds with reactive moieties facilitates downstream diversification and leads to changes in their biological properties. Here, the synthesis of two hydroxy‐bearing allyl pyrophosphates is described. A chemoenzymatic method is demonstrated which uses a promiscuous indole prenyltransferase enzyme to install a dual reactive hydroxy‐bearing allyl moiety directly on the indole ring of tryptophan‐containing peptides. This is the first report of late‐stage indole modifications with this reactive group.
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Affiliation(s)
- Nagaraju Mupparapu
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Lauren Brewster
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Katrina F Ostrom
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy Rinker Health Science Campus, Irvine, CA 92618, USA
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12
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Ledger EVK, Sabnis A, Edwards AM. Polymyxin and lipopeptide antibiotics: membrane-targeting drugs of last resort. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001136. [PMID: 35118938 PMCID: PMC8941995 DOI: 10.1099/mic.0.001136] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
The polymyxin and lipopeptide classes of antibiotics are membrane-targeting drugs of last resort used to treat infections caused by multi-drug-resistant pathogens. Despite similar structures, these two antibiotic classes have distinct modes of action and clinical uses. The polymyxins target lipopolysaccharide in the membranes of most Gram-negative species and are often used to treat infections caused by carbapenem-resistant species such as Escherichia coli, Acinetobacter baumannii and Pseudomonas aeruginosa. By contrast, the lipopeptide daptomycin requires membrane phosphatidylglycerol for activity and is only used to treat infections caused by drug-resistant Gram-positive bacteria such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci. However, despite having distinct targets, both antibiotic classes cause membrane disruption, are potently bactericidal in vitro and share similarities in resistance mechanisms. Furthermore, there are concerns about the efficacy of these antibiotics, and there is increasing interest in using both polymyxins and daptomycin in combination therapies to improve patient outcomes. In this review article, we will explore what is known about these distinct but structurally similar classes of antibiotics, discuss recent advances in the field and highlight remaining gaps in our knowledge.
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Affiliation(s)
- Elizabeth V. K. Ledger
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London, SW7 2AZ, UK
| | - Akshay Sabnis
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London, SW7 2AZ, UK
| | - Andrew M. Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Rd, London, SW7 2AZ, UK
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13
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Johnson BP, Kumar V, Scull EM, Thomas LM, Bourne CR, Singh S. Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus. ACS Chem Biol 2022; 17:85-102. [PMID: 34905349 PMCID: PMC9745668 DOI: 10.1021/acschembio.1c00655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Isopentenyl phosphate kinases (IPKs) catalyze the ATP-dependent phosphorylation of isopentenyl monophosphate (IP) to isopentenyl diphosphate (IPP) in the alternate mevalonate pathways of the archaea and plant cytoplasm. In recent years, IPKs have also been employed in artificial biosynthetic pathways called "(iso) prenol pathways" that utilize promiscuous kinases to sequentially phosphorylate (iso) prenol and generate the isoprenoid precursors IPP and dimethylallyl diphosphate (DMAPP). Furthermore, IPKs have garnered attention for their impressive substrate promiscuity toward non-natural alkyl-monophosphates (alkyl-Ps), which has prompted their utilization as biocatalysts for the generation of novel isoprenoids. However, none of the IPK crystal structures currently available contain non-natural substrates, leaving the roles of active-site residues in substrate promiscuity ambiguous. To address this, we present herein the high-resolution crystal structures of an IPK from Candidatus methanomethylophilus alvus (CMA) in the apo form and bound to natural and non-natural substrates. Additionally, we describe active-site engineering studies leading to enzyme variants with broadened substrate scope, as well as structure determination of two such variants (Ile74Ala and Ile146Ala) bound to non-natural alkyl-Ps. Collectively, our crystallographic studies compare six structures of CMA variants in different ligand-bound forms and highlight contrasting structural dynamics of the two substrate-binding sites. Furthermore, the structural and mutational studies confirm a novel role of the highly conserved DVTGG motif in catalysis, both in CMA and in IPKs at large. As such, the current study provides a molecular basis for the substrate-binding modes and catalytic performance of CMA toward the goal of developing IPKs into useful biocatalysts.
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Affiliation(s)
- Bryce P. Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Vikas Kumar
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Erin M. Scull
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Leonard M. Thomas
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Christina R. Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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14
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Couillaud J, Duquesne K, Iacazio G. Extension of the Terpene Chemical Space: the Very First Biosynthetic Steps. Chembiochem 2021; 23:e202100642. [PMID: 34905641 DOI: 10.1002/cbic.202100642] [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] [Received: 11/19/2021] [Revised: 12/14/2021] [Indexed: 11/06/2022]
Abstract
The structural diversity of terpenes is particularly notable and many studies are carried out to increase it further. In the terpene biosynthetic pathway this diversity is accessible from only two common precursors, i. e. isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Methods recently developed (e. g. the Terpene Mini Path) have allowed DMAPP and IPP to be obtained from a two-step enzymatic conversion of industrially available isopentenol (IOH) and dimethylallyl alcohol (DMAOH) into their corresponding diphosphates. Easily available IOH and DMAOH analogues then offer quick access to modified terpenoids thus avoiding the tedious chemical synthesis of unnatural diphosphates. The aim of this minireview is to cover the literature devoted to the use of these analogues for widening the accessible terpene chemical space.
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Affiliation(s)
- Julie Couillaud
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France.,Actual address: Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Katia Duquesne
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France
| | - Gilles Iacazio
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2 Marseille, CNRS UMR 7313, Av. Escadrille Normandie-Niemen, 13013, Marseille, France
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15
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Kumar V, Johnson BP, Dimas DA, Singh S. Novel Homologs of Isopentenyl Phosphate Kinase Reveal Class-Wide Substrate Flexibility. ChemCatChem 2021; 13:3781-3788. [PMID: 34630731 PMCID: PMC8500459 DOI: 10.1002/cctc.202100595] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 12/26/2022]
Abstract
The widespread utility of isoprenoids has recently sparked interest in efficient synthesis of isoprene-diphosphate precursors. Current efforts have focused on evaluating two-step "isoprenol pathways," which phosphorylate prenyl alcohols using promiscuous kinases/phosphatases. The convergence on isopentenyl phosphate kinases (IPKs) in these schemes has prompted further speculation about the class's utility in synthesizing non-natural isoprenoids. However, the substrate promiscuity of IPKs in general has been largely unexplored. Towards this goal, we report the biochemical characterization of five novel IPKs from Archaea and the assessment of their substrate specificity using 58 alkyl-monophosphates. This study reveals the IPK-catalyzed synthesis of 38 alkyl-diphosphate analogs and discloses broad substrate specificity of IPKs. Further, to demonstrate the biocatalytic utility of IPK-generated alkyl-diphosphates, we also highlight the synthesis of alkyl-l-tryptophan derivatives using coupled IPK-prenyltransferase reactions. These results reveal IPK-catalyzed reactions are compatible with downstream isoprenoid enzymes and further support their development as biocatalytic tools for the synthesis of non-natural isoprenoids.
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Affiliation(s)
- Vikas Kumar
- Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019 (USA)
| | - Bryce P Johnson
- Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019 (USA)
| | - Dustin A Dimas
- Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019 (USA)
| | - Shanteri Singh
- Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019 (USA)
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16
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Moreira R, Wolfe J, Taylor SD. A high-yielding solid-phase total synthesis of daptomycin using a Fmoc SPPS stable kynurenine synthon. Org Biomol Chem 2021; 19:3144-3153. [PMID: 33508054 DOI: 10.1039/d0ob02504f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A high-yielding total synthesis of daptomycin, an important clinical antibiotic, is described. Key to the development of this synthesis was the elucidation of a Camps cyclization reaction that occurs in the solid-phase when conventionally used kynurenine (Kyn) synthons, such as Fmoc-l-Kyn(Boc,CHO)-OH and Fmoc-l-Kyn(CHO,CHO)-OH, are exposed to 20% 2-methylpiperidine (2MP)/DMF. During the synthesis of daptomycin, this side reaction was accompanied by intractable peptide decomposition, which resulted in a low yield of Dap and a 4-quinolone containing peptide. The Camps cyclization was found to occur in solution when Boc-l-Kyn(Boc,CHO)-Ot-Bu and Boc-l-Kyn(CHO,CHO)-OMe were exposed to 20% 2MP/DMF giving the corresponding 4-quinolone amino acid. In contrast, Boc-l-Kyn(CHO)-OMe was stable under these conditions, demonstrating that removing one of the electron withdrawing groups from the aforementioned building blocks prevents enolization in 2MP/DMF. Hence, a new synthesis of daptomycin was developed using Fmoc-l-Kyn(Boc)-OH, which is prepared in two steps from Fmoc-l-Trp(Boc)-OH, that proceeded with an unprecedented 22% overall yield. The simplicity and efficiency of this synthesis will facilitate the preparation of analogs of daptomycin. In addition, the elucidation of this side reaction will simplify preparation of other Kyn-containing natural products via Fmoc SPPS.
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Affiliation(s)
- Ryan Moreira
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, CanadaN2L 3G1.
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Mupparapu N, Lin YHC, Kim TH, Elshahawi SI. Regiospecific Synthesis of Calcium-Independent Daptomycin Antibiotics using a Chemoenzymatic Method. Chemistry 2021; 27:4176-4182. [PMID: 33244806 DOI: 10.1002/chem.202005100] [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] [Received: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Daptomycin (DAP) is a calcium (Ca2+ )-dependent FDA-approved antibiotic drug for the treatment of Gram-positive infections. It possesses a complex pharmacophore hampering derivatization and/or synthesis of analogues. To mimic the Ca2+ -binding effect, we used a chemoenzymatic approach to modify the tryptophan (Trp) residue of DAP and synthesize kinetically characterized and structurally elucidated regiospecific Trp-modified DAP analogues. We demonstrated that the modified DAPs are several times more active than the parent molecule against antibiotic-susceptible and antibiotic-resistant Gram-positive bacteria. Strikingly, and in contrast to the parent molecule, the DAP derivatives do not rely on calcium or any additional elements for activity.
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Affiliation(s)
- Nagaraju Mupparapu
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Yu-Hsin Cindy Lin
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Tae Ho Kim
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA, 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA, 92618, USA
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Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials. Biochem Soc Trans 2021; 49:203-215. [PMID: 33439248 DOI: 10.1042/bst20200425] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure-activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.
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Abstract
Tryprostatin A and B are prenylated, tryptophan-containing, diketopiperazine natural products, displaying cytotoxic activity through different mechanisms of action. The presence of the 6-methoxy substituent on the indole moiety of tryprostatin A was shown to be essential for the dual inhibition of topoisomerase II and tubulin polymerization. However, the inability to perform late-stage modification of the indole ring has limited the structure–activity relationship studies of this class of natural products. Herein, we describe an efficient chemoenzymatic approach for the late-stage modification of tryprostatin B using a cyclic dipeptide N-prenyltransferase (CdpNPT) from Aspergillus fumigatus, which generates novel analogs functionalized with allylic, benzylic, heterocyclic, and diene moieties. Notably, this biocatalytic functionalizational study revealed high selectivity for the indole C6 position. Seven of the 11 structurally characterized analogs were exclusively C6-alkylated, and the remaining four contained predominant C6-regioisomers. Of the 24 accepted substrates, 10 provided >50% conversion and eight provided 20–50% conversion, with the remaining six giving <20% conversion under standard conditions. This study demonstrates that prenyltransferase-based late-stage diversification enables direct access to previously inaccessible natural product analogs.
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