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In silico molecular docking, preclinical evaluation of spiroindimicins A-D, lynamicin A and D isolated from deep marine sea derived Streptomyces sp. SCSIO 03032

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Abstract

The criteria used for successful drug discovery involves high throughput screening for preclinical evaluation and its interaction with target enzymes. In silico approach resulting in the creation of drug like library and identification of essential reactions and pathways spreads across several parts of metabolism. The aim of the present study was to evaluate the preclinical property and interaction to various drug target enzymes for spiroindimicins A-D and lynamicin A and D isolated from deep marine sea derived Streptomyces sp. SCSIO 03032 with 7 selected drug target enzymes. The preclinical and molecular docking simulation was performed using In silico pharmacology and docking tool. Drug likeliness, ADME and toxicity testing findings suggested the compounds with oral drug candidate’s probability. Interaction of isolated compounds against drug target enzymes was satisfactory with Spiroindimicins C, D and Lynamicin D emerging as most potent Topoisomerase II, Cathepsin K, Cytochrome P4503A4, Aromatase P450, protein kinase and histone deacetylase inhibitors. Our results suggest that In silico approach in drug discovery procedure in later stage of development can ease up making lead molecules library.

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References

  1. Amador, M.L., Jimeno, J., Paz-Ares, L., Cortes-Funes, H., Hidalgo, M. 2003. Progress in the development and acquisition of anticancer agents from marine sources. Annals of Oncology 14(11): 1607–1615.

    Article  PubMed  CAS  Google Scholar 

  2. Binkowski, T.A., Naghibzadeh, S., Liang, J. 2003. CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Research 31(13): 3352–3355.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  3. Bowie, J., Luthy, R., Eisenberg, D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253(5016): 164–170.

    Article  PubMed  CAS  Google Scholar 

  4. Bromme, D., Lecaille, F. 2009. Cathepsin K inhibitors for osteoporosis and potential off-target effects. Expert Opinion on Investigational Drugs 18(5): 585–600.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Butler, M.S. 2008. Natural products to drugs: natural product-derived compounds in clinical trials. Nat Prod Rep 25(3): 475–516.

    Article  PubMed  CAS  Google Scholar 

  6. Chun, Y.J., Kim, S. 2003. Discovery of cytochrome P450 1B1 inhibitors as new promising anti-cancer agents. Med Res Rev 23(6): 657–668.

    Article  PubMed  CAS  Google Scholar 

  7. Ekins, S., Mestres, J., Testa, B. 2007. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. Br J Pharmacol 152(1): 9–20.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  8. Fortune, J.M., Osheroff, N. 2000. Topoisomerase II as a target for anticancer drugs: when enzymes stop being nice. Prog Nucleic Acid Res Mol Biol 64: 221–253.

    Article  PubMed  CAS  Google Scholar 

  9. Gani. O.A., Engh, R.A. 2010. Protein kinase inhibition of clinically important staurosporine analogues. Nat Prod Rep 27(4): 489–498.

    Article  PubMed  CAS  Google Scholar 

  10. Ghose, A.K., Viswanadhan, V.N., Wendoloski, J.J. 1998. A Knowledge-Based Approach in Designing Combinatorial or Medicinal Chemistry Libraries for Drug Discovery. 1. A Qualitative and Quantitative Characterization of Known Drug Databases. Journal of Combinatorial Chemistry 1(1): 55–68.

    Article  Google Scholar 

  11. Harvell, C.D., Kim, K., Burkholder, J.M., Colwell, R.R., Epstein, P.R., Grimes, D.J., Hofmann, E.E., Lipp, E.K., Osterhaus, A.D.M.E., Overstreet, R.M., Porter, J.W., Smith, G.W., Vasta, G.R. 1999. Emerging Marine Diseases-Climate Links and Anthropogenic Factors. Science 285(5433): 1505–1510.

    Article  PubMed  CAS  Google Scholar 

  12. Hooft, R.W., Vriend, G., Sander, C., Abola, E.E. 1996. Errors in protein structures. Nature 381(6580): 272.

    Article  PubMed  CAS  Google Scholar 

  13. Hopwood, D.A. 2007. Therapeutic treasures from the deep. Nat Chem Biol 3(8): 457–458.

    Article  PubMed  CAS  Google Scholar 

  14. Imming, P., Sinning, C., Meyer, A. 2006. Opinion-Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov 5: 821–834.

    Article  PubMed  CAS  Google Scholar 

  15. Irvine, J.D., Takahashi, L., Lockhart, K., Cheong, J., Tolan, J.W., Selick, H.E., Grove, J.R. 1999. MDCK (Madin-Darby canine kidney) cells: A tool for membrane permeability screening. J Pharm Sci 88(1): 28–33.

    Article  PubMed  CAS  Google Scholar 

  16. Jensen, P., Fenical, W. 2000. Marine microorganisms and drug discovery: current status and future potential. Drugs from the sea, Basel; New York: Karger. 6–29.

    Chapter  Google Scholar 

  17. Jirage, D.M., Keenan, S.C., Waters, N. 2010. Exploring Novel Targets for Antimalarial Drug Discovery: Plasmodial Protein Kinases. Infectious Disorders-Drug Targets (Formerly Current Drug Targets-Infectious 10(3): 134–146.

    Article  CAS  Google Scholar 

  18. Kramer, J.A.S., John, E., Morris, Dale, L. 2007. The application of discovery toxicology and pathology towards the design of safer pharmaceutical lead candidates. Nat Rev Drug Discov 6(8): 636–649.

    Article  PubMed  CAS  Google Scholar 

  19. Kulkarni, A., Han, Y., Hopfinger, A.J. 2002. Predicting Caco-2 cell permeation coefficients of organic molecules using membrane-interaction QSAR analysis. J Chem Inf Comput Sci 42(2): 331–342.

    Article  PubMed  CAS  Google Scholar 

  20. Lane, A.A., Chabner, B.A. 2009. Histone deacetylase inhibitors in cancer therapy. J Clin Oncol 27(32): 5459–5468.

    Article  PubMed  CAS  Google Scholar 

  21. Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography 26(2): 283–291.

    Article  CAS  Google Scholar 

  22. Lipinski, C.A., Lombardo, F., Dominy, B.W., Feeney, P.J. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews 46(1–3): 3–26.

    Article  PubMed  CAS  Google Scholar 

  23. Macarulla, T., Ramos, F.J., Tabernero, J. 2008. Aurora kinase family: a new target for anticancer drug. Recent Pat Anticancer Drug Discov 3(2): 114–122.

    Article  PubMed  CAS  Google Scholar 

  24. McArthur, K.A., Mitchell, S.S., Tsueng, G., Rheingold, A., White, D.J., Grodberg, J., Lam, K.S., Potts, B.C.M. 2008. Lynamicins A-E, Chlorinated Bisindole Pyrrole Antibiotics from a Novel Marine Actinomyceteâ Journal of Natural Products 71(10): 1732–1737.

    Article  PubMed  CAS  Google Scholar 

  25. Oprea, T. 2000. Property distribution of drugrelated chemical databases*. Journal of Computer-Aided Molecular Design 14(3): 251–264.

    Article  PubMed  CAS  Google Scholar 

  26. Ouaissi, M., Ouaissi, A. 2006. Histone deacetylase enzymes as potential drug targets in cancer and parasitic diseases. J Biomed Biotechnol 2006(2): 13474.

    PubMed  PubMed Central  Google Scholar 

  27. Pandolfi, P.P. 2001. Histone deacetylases and transcriptional therapy with their inhibitors. Cancer Chemother Pharmacol 48Suppl 1: S17–S19.

    Article  PubMed  CAS  Google Scholar 

  28. Ritchie, D.W., Venkatraman, V. 2010. Ultra-fast FFT protein docking on graphics processors. Bioinformatics 26(19): 2398–2405.

    Article  PubMed  CAS  Google Scholar 

  29. Sanchez, C., Mendez, C., Salas, J.A. 2006. Indolocarbazole natural products: occurrence, biosynthesis, and biological activity. Natural Product Reports 23(6): 1007–1045.

    Article  PubMed  CAS  Google Scholar 

  30. Saurav, K., Kannabiran, K. 2011. Interaction of 5-(2, 4-dimethylbenzyl) pyrrolidin-2-one with selected antifungal drug target enzymes by In silico molecular docking studies. Interdisciplinary Sciences: Computational Life Sciences 3(3): 198–203.

    CAS  Google Scholar 

  31. Teague, S.J., Davis, A.M., Leeson, P.D., Oprea, T. 1999. The Design of Leadlike Combinatorial Libraries. Angew Chem Int Ed Engl 38(24): 3743–3748.

    Article  PubMed  CAS  Google Scholar 

  32. Thomas, T., Gallo, M.A., Thomas, T.J. 2004. Estrogen receptors as targets for drug development for breast cancer, osteoporosis and cardiovascular diseases. Curr Cancer Drug Targets 4(6): 483–499.

    Article  PubMed  CAS  Google Scholar 

  33. Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J Mol Graph 8(1): 52–56, 29.

    Article  PubMed  CAS  Google Scholar 

  34. Yefi, R., Ponce, D.P., Niechi, I., Silva, E., Cabello, P., Rodriguez, D.A., Marcelain, K., Armisen, R., Quest, A.F., Tapia, J.C. 2011. Protein kinase CK2 promotes cancer cell viability via upregulation of cyclooxygenase-2 expression and enhanced prostaglandin E2 production. J Cell Biochem 112(11): 3167–3175.

    Article  PubMed  CAS  Google Scholar 

  35. Zhang, W., Liu, Z., Li, S., Yang, T., Zhang, Q., Ma, L., Tian, X., Zhang, H., Huang, C., Zhang, S., Ju, J., Shen, Y., Zhang, C. 2012. Spiroindimicins A-D: new bisindole alkaloids from a deep-sea-derived actinomycete. Org Lett 14(13): 3364–3367.

    Article  PubMed  CAS  Google Scholar 

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Correspondence to Kumar Saurav.

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Saurav, K., Zhang, W., Saha, S. et al. In silico molecular docking, preclinical evaluation of spiroindimicins A-D, lynamicin A and D isolated from deep marine sea derived Streptomyces sp. SCSIO 03032. Interdiscip Sci Comput Life Sci 6, 187–196 (2014). https://doi.org/10.1007/s12539-013-0200-y

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  • DOI: https://doi.org/10.1007/s12539-013-0200-y

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