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image of Isolation and Structural Determination of Cyclic Dipeptides Produced by Arthrobacter sp.

Abstract

Introduction

is a genus of bacteria that has gained recent attention due to its unique ability to produce bioactive compounds that possess potential antimicrobial properties.

Method

In this study, we isolated two cyclic dipeptides (CDPs) from sp. obtained from a soil sample.

Result

The isolated sp. exhibited inhibitory activity against a filamentous indicator bacterium and a violacein-producing sp. Cultivation of sp. TAJX1902 was carried out using rich medium broth and agar to facilitate the extraction of metabolites. The isolated compounds were characterized through spectroscopic techniques. GCMS analysis of the crude extract revealed the presence of bioactive cyclic dipeptides.

Conclusion

The structures of the isolated CDPs were determined as acylated cyclo(D-phenylalanine-4-hydroxy-D-proline) () and cyclo(D-phenylalanine-D-proline) (). Furthermore, two additional metabolites, 2,4-dihydroxypyrimidine () and 2,4-dihydroxy-5-methylpyrimidine (), were identified and verified through NMR spectral analysis.

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2025-01-07
2025-07-03
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References

  1. Antibiotic resistance threats in the United States. 2019 Available from: https://ndc.services.cdc.gov/wp-content/uploads/Antibiotic-Resistance-Threats-in-the-United-States-2019.pdf
  2. Viswanathan V.K. Off-label abuse of antibiotics by bacteria. Gut Microbes 2014 5 1 3 4 10.4161/gmic.28027 24637595
    [Google Scholar]
  3. Munita J.M. Arias C.A. Mechanisms of antibiotic resistance. Microbiol. Spectr. 2016 4 2 4.2.15 10.1128/microbiolspec.VMBF‑0016‑2015 27227291
    [Google Scholar]
  4. Van Boeckel T.P. Gandra S. Ashok A. Caudron Q. Grenfell B.T. Levin S.A. Laxminarayan R. Global antibiotic consumption 2000 to 2010: An analysis of national pharmaceutical sales data. Lancet Infect. Dis. 2014 14 8 742 750 10.1016/S1473‑3099(14)70780‑7 25022435
    [Google Scholar]
  5. Rossiter S.E. Fletcher M.H. Wuest W.M. Natural products as platforms to overcome antibiotic resistance. Chem. Rev. 2017 117 19 12415 12474 10.1021/acs.chemrev.7b00283 28953368
    [Google Scholar]
  6. McMurry L. Petrucci R.E. Levy S.B. Active efflux of tetracycline encoded by four genetically different tetracycline resistance determinants in Escherichia coli. Proc. Natl. Acad. Sci. USA 1980 77 7 3974 3977 10.1073/pnas.77.7.3974 7001450
    [Google Scholar]
  7. Barton D. Meth-Cohn O. Comprehensive Natural Products Chemistry 1st ed Newnes 1999
    [Google Scholar]
  8. Chibale K. Economic drug discovery and rational medicinal chemistry for tropical diseases. Pure Appl. Chem. 2005 77 11 1957 1964 10.1351/pac200577111957
    [Google Scholar]
  9. Demain A.L. Importance of microbial natural products and the need to revitalize their discovery. J. Ind. Microbiol. Biotechnol. 2014 41 2 185 201 10.1007/s10295‑013‑1325‑z 23990168
    [Google Scholar]
  10. Newman D.J. Cragg G.M. Snader K.M. Natural products as sources of new drugs over the period 1981-2002. J. Nat. Prod. 2003 66 7 1022 1037 10.1021/np030096l 12880330
    [Google Scholar]
  11. Cragg G.M. Newman D.J. Natural products: A continuing source of novel drug leads. Biochim. Biophys. Acta, Gen. Subj. 2013 1830 6 3670 3695 10.1016/j.bbagen.2013.02.008 23428572
    [Google Scholar]
  12. Abdel-Razek A.S. El-Naggar M.E. Allam A. Morsy O.M. Othman S.I. Microbial natural products in drug discovery. Processes (Basel) 2020 8 4 470 10.3390/pr8040470
    [Google Scholar]
  13. Hu Y. Phelan V. Ntai I. Farnet C.M. Zazopoulos E. Bachmann B.O. Benzodiazepine biosynthesis in Streptomyces refuineus. Chem. Biol. 2007 14 6 691 701 10.1016/j.chembiol.2007.05.009 17584616
    [Google Scholar]
  14. Ntie-Kang F. Svozil D. An enumeration of natural products from microbial, marine and terrestrial sources. Phys. Sci. Rev. 2020 5 8 20180121 10.1515/psr‑2018‑0121
    [Google Scholar]
  15. Kramer J. Özkaya Ö. Kümmerli R. Bacterial siderophores in community and host interactions. Nat. Rev. Microbiol. 2020 18 3 152 163 10.1038/s41579‑019‑0284‑4 31748738
    [Google Scholar]
  16. Manivasagan P. Venkatesan J. Sivakumar K. Kim S.K. Pharmaceutically active secondary metabolites of marine actinobacteria. Microbiol. Res. 2014 169 4 262 278 10.1016/j.micres.2013.07.014 23958059
    [Google Scholar]
  17. Dang T. Süssmuth R.D. Bioactive peptide natural products as lead structures for medicinal use. Acc. Chem. Res. 2017 50 7 1566 1576 10.1021/acs.accounts.7b00159 28650175
    [Google Scholar]
  18. Wang J. Zhang R. Chen X. Sun X. Yan Y. Shen X. Yuan Q. Biosynthesis of aromatic polyketides in microorganisms using type II polyketide synthases. Microb. Cell Fact. 2020 19 1 110 10.1186/s12934‑020‑01367‑4 32448179
    [Google Scholar]
  19. Zhao P. Xue Y. Gao W. Li J. Zu X. Fu D. Feng S. Bai X. Zuo Y. Li P. Actinobacteria–derived peptide antibiotics since 2000. Peptides 2018 103 48 59 10.1016/j.peptides.2018.03.011 29567053
    [Google Scholar]
  20. Walsh C.T. O’Brien R.V. Khosla C. Nonproteinogenic amino acid building blocks for nonribosomal peptide and hybrid polyketide scaffolds. Angew. Chem. Int. Ed. 2013 52 28 7098 7124 10.1002/anie.201208344 23729217
    [Google Scholar]
  21. Ortega M.A. van der Donk W.A. New insights into the biosynthetic logic of ribosomally synthesized and post-translationally modified peptide natural products. Cell Chem. Biol. 2016 23 1 31 44 10.1016/j.chembiol.2015.11.012 26933734
    [Google Scholar]
  22. Walker J.A. Hamlish N. Tytla A. Brauer D.D. Francis M.B. Schepartz A. Redirecting RiPP biosynthetic enzymes to proteins and backbone-modified substrates. ACS Cent. Sci. 2022 8 4 473 482 10.1021/acscentsci.1c01577 35505866
    [Google Scholar]
  23. Imani A.S. Freeman M.F. RiPPing apart the rules for peptide natural products. Synth. Syst. Biotechnol. 2018 3 2 81 82 10.1016/j.synbio.2018.03.002 29900419
    [Google Scholar]
  24. Andrew B. Scott L. Practical Medicinal Chemistry with Macrocycles. Marsault E. Peterson M.L. Hoboken, NJ, USA John Wiley & Sons, Inc. 2017 10.1002/9781119092599
    [Google Scholar]
  25. Dandapani S. Marcaurelle L.A. Grand Challenge Commentary: Accessing new chemical space for ‘undruggable’ targets. Nat. Chem. Biol. 2010 6 12 861 863 10.1038/nchembio.479 21079589
    [Google Scholar]
  26. Joo S.H. Cyclic peptides as therapeutic agents and biochemical tools. Biomol. Ther. (Seoul) 2012 20 1 19 26 10.4062/biomolther.2012.20.1.019 24116270
    [Google Scholar]
  27. Bhat A. Roberts L.R. Dwyer J.J. Lead discovery and optimization strategies for peptide macrocycles. Eur. J. Med. Chem. 2015 94 471 479 10.1016/j.ejmech.2014.07.083 25109255
    [Google Scholar]
  28. Park S.C. Park Y. Hahm K.S. The role of antimicrobial peptides in preventing multidrug-resistant bacterial infections and biofilm formation. Int. J. Mol. Sci. 2011 12 9 5971 5992 10.3390/ijms12095971 22016639
    [Google Scholar]
  29. Kitagaki J. Shi G. Miyauchi S. Murakami S. Yang Y. Cyclic depsipeptides as potential cancer therapeutics. Anticancer Drugs 2015 26 3 259 271 10.1097/CAD.0000000000000183 25419631
    [Google Scholar]
  30. Gavrish E. Sit C.S. Cao S. Kandror O. Spoering A. Peoples A. Ling L. Fetterman A. Hughes D. Bissell A. Torrey H. Akopian T. Mueller A. Epstein S. Goldberg A. Clardy J. Lewis K. Lassomycin, a ribosomally synthesized cyclic peptide, kills mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. Chem. Biol. 2014 21 4 509 518 10.1016/j.chembiol.2014.01.014 24684906
    [Google Scholar]
  31. Risdian C. Mozef T. Wink J. Biosynthesis of polyketides in Streptomyces. Microorganisms 2019 7 5 124 10.3390/microorganisms7050124 31064143
    [Google Scholar]
  32. Ling L.L. Schneider T. Peoples A.J. Spoering A.L. Engels I. Conlon B.P. Mueller A. Schäberle T.F. Hughes D.E. Epstein S. Jones M. Lazarides L. Steadman V.A. Cohen D.R. Felix C.R. Fetterman K.A. Millett W.P. Nitti A.G. Zullo A.M. Chen C. Lewis K. A new antibiotic kills pathogens without detectable resistance. Nature 2015 517 7535 455 459 10.1038/nature14098 25561178
    [Google Scholar]
  33. Ranjani A. Dhanasekaran D. Gopinath P.M. An introduction to actinobacteria. Actinobacteria - Basics and Biotechnological Applications IntechOpen Dhanasekaran D. Jiang Y. 2016 10.5772/62329
    [Google Scholar]
  34. Igarashi Y. Yamamoto K. Fukuda T. Shojima A. Nakayama J. Carro L. Trujillo M.E. Arthroamide, a cyclic depsipeptide with quorum sensing inhibitory activity from Arthrobacter sp. J. Nat. Prod. 2015 78 11 2827 2831 10.1021/acs.jnatprod.5b00540 26575343
    [Google Scholar]
  35. Busse H.J. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter roseus. Int. J. Syst. Evol. Microbiol. 2016 66 1 9 37 10.1099/ijsem.0.000702 26486726
    [Google Scholar]
  36. Mawlankar R.B. Dharne M.S. Dastager S.G. Isolation of potent alpha-glucosidase inhibitor from a novel marine bacterium Arthrobacter enclensis. SN Appl. Sci. 2020 2 3 474 10.1007/s42452‑020‑2285‑3
    [Google Scholar]
  37. Ramlawi S. Aitken A. Abusharkh S. McMullin D.R. Avis T.J. Arthropeptide A, an antifungal cyclic tetrapeptide from Arthrobacter psychrophenolicus isolated from disease suppressive compost. Nat. Prod. Res. 2022 36 22 5715 5723 10.1080/14786419.2021.2018434 34933636
    [Google Scholar]
  38. Munaganti R.K. Muvva V. Konda S. Naragani K. Mangamuri U.K. Dorigondla K.R. Akkewar D.M. Antimicrobial profile of Arthrobacter kerguelensis VL-RK_09 isolated from Mango orchards. Braz. J. Microbiol. 2016 47 4 1030 1038 10.1016/j.bjm.2016.07.010 27515463
    [Google Scholar]
  39. Kanoh K. Kohno S. Asari T. Harada T. Katada J. Muramatsu M. Kawashima H. Sekiya H. Uno I. (−)-Phenylahistin: A new mammalian cell cycle inhibitor produced by aspergillus ustus. Bioorg. Med. Chem. Lett. 1997 7 22 2847 2852 10.1016/S0960‑894X(97)10104‑4
    [Google Scholar]
  40. Hayashi Y. Yamazaki-Nakamura Y. Yakushiji F. Medicinal chemistry and chemical biology of diketopiperazine-type antimicrotubule and vascular-disrupting agents. Chem. Pharm. Bull. (Tokyo) 2013 61 9 889 901 10.1248/cpb.c13‑00404 23995353
    [Google Scholar]
  41. Cui C.B. Kakeya H. Okada G. Onose R. Osada H. Novel mammalian cell cycle inhibitors, tryprostatins A, B and other diketopiperazines produced by Aspergillus fumigatus. I. Taxonomy, fermentation, isolation and biological properties. J. Antibiot. (Tokyo) 1996 49 6 527 533 10.7164/antibiotics.49.527 8698634
    [Google Scholar]
  42. Zhao S. Smith K.S. Deveau A.M. Dieckhaus C.M. Johnson M.A. Macdonald T.L. Cook J.M. Biological activity of the tryprostatins and their diastereomers on human carcinoma cell lines. J. Med. Chem. 2002 45 8 1559 1562 10.1021/jm0155953 11931609
    [Google Scholar]
  43. Kumar N. Mohandas C. Nambisan B. Kumar D.R.S. Lankalapalli R.S. Isolation of proline-based cyclic dipeptides from Bacillus sp. N strain associated with rhabitid entomopathogenic nematode and its antimicrobial properties. World J. Microbiol. Biotechnol. 2013 29 2 355 364 10.1007/s11274‑012‑1189‑9 23065379
    [Google Scholar]
  44. Liu H. An M. Si H. Shan Y. Xu C. Hu G. Xie Y. Liu D. Li S. Qiu R. Zhang C. Wu Y. Identification of cyclic dipeptides and a new compound (6-(5-hydroxy-6-methylheptyl)-5,6-dihydro-2H-pyran-2-one) produced by Streptomyces fungicidicus against Alternaria solani. Molecules 2022 27 17 5649 10.3390/molecules27175649 36080412
    [Google Scholar]
  45. Wang G. Dai S. Chen M. Wu H. Xie L. Luo X. Li X. Two diketopiperazine cyclo(pro-phe) isomers from marine bacteria Bacillus subtilis sp. 13-2. Chem. Nat. Compd. 2010 46 4 583 585 10.1007/s10600‑010‑9680‑8
    [Google Scholar]
  46. Fu S. Zhang Y. Yang C. Meng Q. Preparation of uracil by bacteria isolated from Morchella. Pak. J. Pharm. Sci. 2020 33 2 621 625 32276907
    [Google Scholar]
  47. Huang D.Y. Nong X.H. Zhang Y.Q. Xu W. Sun L.Y. Zhang T. Chen G.Y. Han C.R. Two new 2,5-diketopiperazine derivatives from mangrove-derived endophytic fungus Nigrospora camelliae-sinensis S30. Nat. Prod. Res. 2022 36 14 3651 3656 10.1080/14786419.2021.1878168 33517796
    [Google Scholar]
  48. Ström K. Sjögren J. Broberg A. Schnürer J. Lactobacillus plantarum MiLAB 393 produces the antifungal cyclic dipeptides cyclo(L-Phe-L-Pro) and cyclo(L-Phe-trans-4-OH-L-Pro) and 3-phenyllactic acid. Appl. Environ. Microbiol. 2002 68 9 4322 4327 10.1128/AEM.68.9.4322‑4327.2002 12200282
    [Google Scholar]
  49. Sun S.J. Liu Y.C. Weng C.H. Sun S.W. Li F. Li H. Zhu H. Cyclic dipeptides mediating quorum sensing and their biological effects in hypsizygus marmoreus. Biomolecules 2020 10 2 298 10.3390/biom10020298 32070027
    [Google Scholar]
  50. Holden M.T.G. Ram Chhabra S. De Nys R. Stead P. Bainton N.J. Hill P.J. Manefield M. Kumar N. Labatte M. England D. Rice S. Givskov M. Salmond G.P.C. Stewart G.S.A.B. Bycroft B.W. Kjelleberg S. Williams P. Quorum‐sensing cross talk: Isolation and chemical characterization of cyclic dipeptides from Pseudomonas aeruginosa and other Gram‐negative bacteria. Mol. Microbiol. 1999 33 6 1254 1266 10.1046/j.1365‑2958.1999.01577.x 10510239
    [Google Scholar]
  51. Ledderhof N.J. Caminiti M.F. Bradley G. Lam D.K. Topical 5-fluorouracil is a novel targeted therapy for the keratocystic odontogenic tumor. J. Oral Maxillofac. Surg. 2017 75 3 514 524 10.1016/j.joms.2016.09.039 27789270
    [Google Scholar]
  52. Fan L. Pan Z. Liao X. Zhong Y. Guo J. Pang R. Chen X. Ye G. Su Y. Uracil restores susceptibility of methicillin-resistant Staphylococcus aureus to aminoglycosides through metabolic reprogramming. Front. Pharmacol. 2023 14 1133685 10.3389/fphar.2023.1133685 36762116
    [Google Scholar]
  53. Liu Y. Yang K. Jia Y. Shi J. Tong Z. Wang Z. Thymine sensitizes gram-negative pathogens to antibiotic killing. Front. Microbiol. 2021 12 622798 10.3389/fmicb.2021.622798 33584625
    [Google Scholar]
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  • Article Type:
    Research Article
Keywords: Arthrobacter ; soil bacteria ; Cyclic dipeptides ; bioactivity ; metabolites
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