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Aguilar C, Verdel-Aranda K, Ramos-Aboites HE, Licona-Cassani C, Barona-Gómez F. Streptomyces lividans 66 produces a protease inhibitor via a tRNA-utilizing enzyme interacting with a C-minus NRPS. J Ind Microbiol Biotechnol 2023; 50:kuad021. [PMID: 37669898 PMCID: PMC10548850 DOI: 10.1093/jimb/kuad021] [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: 05/25/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023]
Abstract
Small peptide aldehydes (SPAs) with protease inhibitory activity are naturally occurring compounds shown to be synthesized by non-ribosomal peptide synthetases (NRPS). SPAs are widely used in biotechnology and have been utilized as therapeutic agents. They are also physiologically relevant and have been postulated to regulate the development of their producing microorganisms. Previously, we identified an NRPS-like biosynthetic gene cluster (BGC) in Streptomyces lividans 66 that lacked a condensation (C) domain but included a tRNA-utilizing enzyme (tRUE) belonging to the leucyl/phenylalanyl (L/F) transferase family. This system was predicted to direct the synthesis of a novel SPA, which we named livipeptin. Using evolutionary genome mining approaches, here, we confirm the presence of L/F transferase tRUEs within the genomes of diverse Streptomyces and related organisms, including fusions with the anticipated C-minus NRPS-like protein. We then demonstrate genetic functional cooperation between the identified L/F-transferase divergent tRUE homolog with the C-minus NRPS, leading to the synthesis of a metabolic fraction with protease inhibitory activity. Semisynthetic assays in the presence of RNAse revealed that the productive interaction between the tRUE and the C-minus NRPS enzymes is indeed tRNA dependent. We expect our findings to boost the discovery of SPAs, as well as the development of protease-mediated biotechnologies, by exploiting the uncovered genetic basis for synthesizing putative acetyl-leu/phe-arginine protease inhibitors. Furthermore, these results will facilitate the purification and structural elucidation of livipeptin, which has proven difficult to chemically characterize. SIGNIFICANCE The discovery of natural products biosynthetic genes marks a significant advancement in our understanding of these metabolites, for example of their evolution, activity, and biosynthesis, but also opens biotechnological opportunities and knowledge to advance genome mining approaches. We made this possible by uncovering a new biosynthetic pathway in Streptomyces lividans 66 shown to direct the synthesis of a strong protease inhibitor, termed livipeptin, following unprecedented biosynthetic rules and genes. Thus, by shedding light on the genetic mechanisms predicted to govern the production of acetyl-leu/phe-arginine protease inhibitors, including the elusive livipeptin, this study enables novel protease-mediated biotechnologies as well as approaches for discovering protease inhibitors from genome data.
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Affiliation(s)
- César Aguilar
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Karina Verdel-Aranda
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Hilda E Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Cuauhtémoc Licona-Cassani
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Irapuato, Guanajuato, CP 36821, México
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Ramachandra SN, Srinivasulu C, Hosamani B, L S, Sureshbabu VV. A Simple, Mild and Straight forward Route for the Synthesis of α‐Ureidopeptidomimetics Using Cbz‐Protected Amino Acid Esters. ChemistrySelect 2018. [DOI: 10.1002/slct.201802892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sagar N. Ramachandra
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - C. Srinivasulu
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - Basavaprabhu Hosamani
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - Santhosh L
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
| | - Vommina V. Sureshbabu
- # 109, Peptide Research LaboratoryDepartment of Studies in ChemistryCentral College CampusBangalore University Bangalore-560001 India
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Manne SR, Thalluri K, Giri RS, Chandra J, Mandal B. Ethyl 2-(tert-Butoxycarbonyloxyimino)-2-cyanoacetate (Boc-Oxyma): An Efficient Reagent for the Racemization Free Synthesis of Ureas, Carbamates and Thiocarbamates via Lossen Rearrangement. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600661] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Srinivasa Rao Manne
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati Assam - 781039 India
| | - Kishore Thalluri
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati Assam - 781039 India
| | - Rajat Subhra Giri
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati Assam - 781039 India
| | - Jyoti Chandra
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati Assam - 781039 India
| | - Bhubaneswar Mandal
- Department of Chemistry; Indian Institute of Technology Guwahati; Guwahati Assam - 781039 India
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Ke D, Zhan C, Li X, Li AD, Yao J. The urea-dipeptides show stronger H-bonding propensity to nucleate β-sheetlike assembly than natural sequence. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.07.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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The imide-dipeptides that show strong and stable β-sheet-like interactions compared with natural sequence. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.04.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Sureshbabu VV, Patil BS, Venkataramanarao R. Preparation, isolation, and characterization of Nalpha-Fmoc-peptide isocyanates: solution synthesis of oligo-alpha-peptidyl ureas. J Org Chem 2007; 71:7697-705. [PMID: 16995676 DOI: 10.1021/jo0611723] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The N(alpha)-Fmoc-peptide isocyanates 3a-q, 4a-c, and 5a-c were prepared by the Curtius rearrangement of N(alpha)-Fmoc-peptide acid azides in toluene under thermal, microwave, and ultrasonic conditions. All the N(alpha)-Fmoc-oligo-peptide isocyanates made were isolated as stable crystalline solids with 71 to 94% yield and were fully characterized by 1H NMR, 13C NMR, and mass spectroscopy. Their utility for the synthesis of oligo-alpha-peptidyl ureas 7a-f and 8a-c by the divergent coupling approach was demonstrated. The coupling of N(alpha)-Fmoc-dipeptide isocyanates with amino acid ester or with N,O-bis(trimethylsilyl)amino acids resulted in N(alpha)-Fmoc-tripeptidyl urea ester and acids containing one each of peptide bond and urea bond. The divergent approach is extended to the synthesis of tetrapeptidyl ureas by the 2 + 2 strategy using bis-TMS-peptide acid as an amino component. To incorporate urea bonds in adjacent positions, N(alpha)-Fmoc-peptidyl urea isocyanates 9a-d were prepared and employed in the synthesis of three tetrapeptidyl ureas 10a-b and 11 containing one peptide bond and two urea bonds in series from the N-terminal end. The protocol was then employed for the synthesis of five urea analogues 13-15, 18, and 21 of [Leu5]enkephalin containing urea bonds at the 2, 3, 4 positions as well as at the 2, 4 and 2, 3, 4 positions. The analogue 2l was made by the convergent synthesis by the N --> C terminal chain extension. Finally, two urea analogues 22 and 23 of repeat units of bioelasto polymers, namely Val-Pro-Gly-Val-Gly-OH and Pro-Gly-Val-Gly-Val-OH, were synthesized incorporating the urea bond by the concomitant isocyanate generation and urea bond formation under thermal conditions.
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Affiliation(s)
- Vommina V Sureshbabu
- Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore 560 001, India.
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Bouzide A, Sauvé G. Synthesis of N-acyl-β-aminoalcohols from N-acyloxazolidinones mediated by sodium azide. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)00155-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Konda Y, Takahashi Y, Arima S, Sato N, Takeda K, Dobashi K, Baba M, Harigaya Y. First total synthesis of Mer-N5075A and a diastereomeric mixture of α and β-MAPI, new HIV-I protease inhibitors from a species of Streptomyces. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00323-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Page P, Bradley M, Walters I, Teague S. Solid-Phase Synthesis of Tyrosine Peptide Aldehydes. Analogues of (S)-MAPI. J Org Chem 1999; 64:794-799. [PMID: 11674148 DOI: 10.1021/jo981546v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report an efficient solid-phase synthesis of C-terminal tyrosine peptide aldehydes based on the HIV protease inhibitors (S)-MAPI and GE 20372 A. Our strategy consisted of anchoring the side chain of Dde-Tyrosinol (5) onto the brominated Wang linker derivative ((4-bromomethyl)-phenoxy-allyl acetate) (6) to give after ester hydrolysis the N(alpha)-(Dde)-O-(4-methylphenoxyacetic acid)-L-Tyrosinol template (8). This was attached to aminomethyl resin and elongated using standard Fmoc protocols. Importantly there was no evidence of esterification side reactions. The unsymmetrically substituted urea linkage of the (S)-MAPI family was incorporated using the N(alpha)-(4-nitrophenyloxycarbonyl)amino acid tert-butyl esters following which the protected tetrapeptide alcohol immobilized on the solid support was oxidized to its corresponding aldehyde using sulfur trioxide-pyridine. The efficiency and reliability of the oxidation step was dramatically improved by the incorporation of a small PEG-spacer between the linker and the solid support. The tetrapeptides 12a and 12b were cleaved by acidolysis, purified by RP HPLC, and isolated in high yield and purity, demonstrating the success of the whole synthetic process.
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Affiliation(s)
- Patrick Page
- Department of Medicinal Chemistry, Astra Charnwood, Bakewell Road, Loughborough, Leicestershire, LE11 ORH, UK
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Zhang X, Rodrigues J, Evans L, Hinkle B, Ballantyne L, Peña M. Formation of Urea Dipeptides from Carbonyldiimidazole: Application toward the Protease Inhibitors GE 20372 and MAPI. J Org Chem 1997. [DOI: 10.1021/jo970514p] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaowei Zhang
- Department of Chemistry and Biochemistry, Arizona State University, Box 871604, Tempe, Arizona 85287-1604
| | - Jason Rodrigues
- Department of Chemistry and Biochemistry, Arizona State University, Box 871604, Tempe, Arizona 85287-1604
| | - Lawrence Evans
- Department of Chemistry and Biochemistry, Arizona State University, Box 871604, Tempe, Arizona 85287-1604
| | - Becky Hinkle
- Department of Chemistry and Biochemistry, Arizona State University, Box 871604, Tempe, Arizona 85287-1604
| | - Lisa Ballantyne
- Department of Chemistry and Biochemistry, Arizona State University, Box 871604, Tempe, Arizona 85287-1604
| | - Michael Peña
- Department of Chemistry and Biochemistry, Arizona State University, Box 871604, Tempe, Arizona 85287-1604
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Konda Y, Takahashi Y, Mita H, Takeda K, Harigaya Y. First Total Synthesis of Mer-N5075A, A New HIV-I Protease Inhibitor fromStreptomyces Chromofuscus. CHEM LETT 1997. [DOI: 10.1246/cl.1997.345] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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