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Structural and functional characterization of the Vindoline biosynthesis pathway enzymes of Catharanthus roseus

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Abstract

Vinblastine and its related compound vincristine are important mono terpenoid indole alkaloids accumulated in the leaves of Catharanthus roseus (Madagascar periwinkle). They serve as major anticancer drugs. Vinblastine is formed by the condensation of vindoline and catharanthine. The vindoline moiety is derived from tabersonine via vindoline biosynthesis pathway. The reaction sequence from tabersonine to vindoline is now well established and the enzymes involved in this pathway are identified. However, to date, the structures of the enzymes involved in the vindoline biosynthesis pathway are not known, leading to limited mechanistic understanding of the substrate binding and catalysis. The purpose of this work is to provide structural insight regarding all the steps of the vindoline pathway via rigorous homology modeling, molecular docking, and molecular dynamics analyses. Substrate and cofactors required for each step were docked onto the computationally built and validated three-dimensional (3D) model of the corresponding enzyme, and the catalytic reaction was analyzed from the structural point of view. Possible binding modes of the substrates and cofactors were generated and corresponding binding residues were identified. Enzyme-substrate models were verified based on structure evaluation methods and molecular dynamics based approaches. Findings of our analysis would be useful in rational designing of these important enzymes aimed toward bio-production of vindoline.

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References

  1. Negi A, Singla R, Singh V (2014) Indole based alkaloid in cancer: an overview. PharmaTutor 2:76–82

    Google Scholar 

  2. Noble RL (1990) The discovery of the vinca alkaloids--chemotherapeutic agents against cancer. Biochem Cell Biol 68(12):1344–1351

    Article  CAS  Google Scholar 

  3. Zu YG, Luo M, Mu FS, Fu YJ, Wang L (2006) Advances on alkaloids in Catharanthusroseus and theirpharmacological activities. Nat Prod Res Dev (18):325–329

  4. Qu Y, Easson ML, Froese J, Simionescu R, Hudlicky T, De Luca V (2015) Completion of the seven-step pathway from tabersonine to the anticancer drug precursor vindoline and its assembly in yeast. Proc Natl Acad Sci U S A 112(19):6224–6229. https://doi.org/10.1073/pnas.1501821112

    Article  CAS  Google Scholar 

  5. Sottomayor M, Duarte P, Figueiredo R, RosBarcelo A (2008) A vacuolar class III peroxidase and the metabolism of anticancer indole alkaloids in Catharanthusroseus: can peroxidases, secondary metabolites and arabinogalactan proteins be partners in microcompartmentation of cellular reactions? Plant Signal Behav 3(10):899–901

    Article  Google Scholar 

  6. O’Connor SE, Maresh JJ (2006) Chemistry and biology of monoterpeneindole alkaloid biosynthesis. Nat Prod Rep 23(4):532–547. https://doi.org/10.1039/b512615k

    Article  Google Scholar 

  7. UniProt: the universal protein knowledgebase (2017). Nucleic Acids Res. 45(D1):D158–D169. https://doi.org/10.1093/nar/gkw1099

    Article  Google Scholar 

  8. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 32(Database issue):D431–D433. https://doi.org/10.1093/nar/gkh081

    Article  CAS  Google Scholar 

  9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2S0022-2836(05)

    Article  CAS  Google Scholar 

  10. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Soding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Mol Syst Biol 7:539. https://doi.org/10.1038/msb.2011.75

    Article  Google Scholar 

  11. Pei J, Grishin NV (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17(8):700–712

    Article  CAS  Google Scholar 

  12. Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue):W244–W248

    Article  Google Scholar 

  13. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845–858. https://doi.org/10.1038/nprot.2015.053

    Article  CAS  Google Scholar 

  14. McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4):404–405

    Article  CAS  Google Scholar 

  15. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815. https://doi.org/10.1006/jmbi.1993.1626

    Article  CAS  Google Scholar 

  16. Lovell SC, Davis IW, Arendall 3rd WB, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50(3):437–450. https://doi.org/10.1002/prot.10286

    Article  CAS  Google Scholar 

  17. Luthy R, Bowie JU, Eisenberg D (1992) Assessment of protein models with three-dimensional profiles. Nature 356(6364):83–85. https://doi.org/10.1038/356083a0

    Article  CAS  Google Scholar 

  18. Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2(9):1511–1519. https://doi.org/10.1002/pro.5560020916

    Article  CAS  Google Scholar 

  19. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera--a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. https://doi.org/10.1002/jcc.20084

    Article  CAS  Google Scholar 

  20. Sali A (1995) Comparative protein modeling by satisfaction of spatial restraints. Mol Med Today 1(6):270–277

    Article  CAS  Google Scholar 

  21. Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245(1):43–53

    Article  CAS  Google Scholar 

  22. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267(3):727–748. https://doi.org/10.1006/jmbi.1996.0897

    Article  CAS  Google Scholar 

  23. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261(3):470–489. https://doi.org/10.1006/jmbi.1996.0477

    Article  CAS  Google Scholar 

  24. James JP, Stewart (2016) MOPAC2016, Stewart Computational Chemistry, Colorado Springs, CO. http://OpenMOPAC.net 2016

  25. Cao Y, Li L (2014) Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model. Bioinformatics 30:1674–1680

    Article  CAS  Google Scholar 

  26. Kevin JB,Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossváry I, Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE (2006) Scalable algorithms for molecular dynamics simulations on commodity Clusters. Proceedings of the ACM/IEEE conference on supercomputing (SC06), Tampa, FL, 11–17Nov 2006

  27. Jorgensen W L,Maxwell D S,Tirado R J (1996) Development and testing of the OPLS all-atomforce field on conformational energetics and properties of organic liquids. J Am Chem Soc (118):11225–11236

  28. Kaminski G, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparameterizationof the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations onpeptides. J Phys Chem B 105:6474–6487

    Article  CAS  Google Scholar 

  29. Levy RM (2005) The OPLS_2005 parameters are described in Banks. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comp Chem (26): 1752

  30. Maxwell S (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Connecticut 06520–8107

  31. McAliley JH, Bruce DA (2011) Development of force field parameters for molecular simulation of polylactide. J Chem Theory Comput 7(11):3756–3767. https://doi.org/10.1021/ct200251x

    Article  CAS  Google Scholar 

  32. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

    Article  CAS  Google Scholar 

  33. Nose S (1984) A unified formulation of the constant temperature molecular dynamics methods. J Chem Phys (81): 511

  34. Martyna GJ, Tobias DJ, Klein ML (1994) Constant pressure molecular dynamics algorithms. J Chem Phys 101:4177–4189

    Article  CAS  Google Scholar 

  35. Tuckerman M, Berne BJ, Martyna GJ (1992) Reversible multiple time scale molecular dynamics. J Chem Phys 97:1990–2001

    Article  CAS  Google Scholar 

  36. Liu CJ, Deavours BE, Richard SB, Ferrer JL, Blount JW, Huhman D, Dixon RA, Noel JP (2006) Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. Plant Cell 18(12):3656–3669. https://doi.org/10.1105/tpc.106.041376

    Article  CAS  Google Scholar 

  37. DeVore NM, Scott EE (2012) Structures of cytochrome P450 17A1 with prostate cancer drugs abiraterone and TOK-001. Nature 482(7383):116–119. https://doi.org/10.1038/nature10743

    Article  CAS  Google Scholar 

  38. Singh S, McCoy JG, Zhang C, Bingman CA, Phillips Jr GN, Thorson JS (2008) Structure and mechanism of the rebeccamycin sugar 4′-O-methyltransferase RebM. J Biol Chem 283(33):22628–22636. https://doi.org/10.1074/jbc.M800503200

    Article  CAS  Google Scholar 

  39. Wilmouth RC, Turnbull JJ, Welford RW, Clifton IJ, Prescott AG, Schofield CJ (2002) Structure and mechanism of anthocyanidin synthase from Arabidopsis Thaliana. Structure 10(1):93–103

    Article  CAS  Google Scholar 

  40. De Carolis E, De Luca V (1993) Purification, characterization, and kinetic analysis of a 2-oxoglutarate-dependent dioxygenase involved in vindoline biosynthesis from Catharanthusroseus. J BiolChem 268(8):5504–5511

    Google Scholar 

  41. Ma X, Koepke J, Panjikar S, Fritzsch G, Stockigt J (2005) Crystal structure of vinorine synthase, the first representative of the BAHD superfamily. J Biol Chem 280(14):13576–13583. https://doi.org/10.1074/jbc.M414508200

    Article  CAS  Google Scholar 

  42. Gigant B, Wang C, Ravelli RB, Roussi F, Steinmetz MO, Curmi PA, Sobel A, Knossow M (2005) Structural basis for the regulation of tubulin by vinblastine. Nature 435(7041):519–522. https://doi.org/10.1038/nature03566

    Article  CAS  Google Scholar 

Download references

Acknowledgments

SC acknowledges CSIR-IICB for infrastructural support and Department of Biotechnology for Ramalingaswami fellowship. The work is supported by CSIR network projects funds (HCP002 and BSC0121).

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Author notes

  1. Bilal Ahmad and Anindyajit Banerjee contributed equally to this work.

Authors and Affiliations

  1. Department of Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research, CSIR-Indian Institute of Chemical Biology, Kolkata, WB, India

    Bilal Ahmad, Anindyajit Banerjee, Harshita Tiwari, Shrabasti Jana, Sudeshna Bose & Saikat Chakrabarti

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  1. Bilal Ahmad
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  2. Anindyajit Banerjee
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Correspondence to Saikat Chakrabarti.

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Ahmad, B., Banerjee, A., Tiwari, H. et al. Structural and functional characterization of the Vindoline biosynthesis pathway enzymes of Catharanthus roseus. J Mol Model 24, 53 (2018). https://doi.org/10.1007/s00894-018-3590-2

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