Combined pharmacophore-guided 3D-QSAR, molecular docking, and virtual screening on bis-benzimidazoles and ter-benzimidazoles as DNA–topoisomerase I poisons

  • Upasana Issar
  • Richa Arora
  • Tripti Kumari
  • Rita KakkarEmail author
Original Research


Certain DNA minor groove binders, especially bis-benzimdazole containing compounds, such as Hoechst 33258 and its derivatives, act as potent topoisomerase I inhibitors. The mechanism of action of these drugs is complex and involves hindering the breakage/reunion reaction of topoisomerase I. In the present work, molecular modeling studies have been performed to develop a pharmacophore and 3D-quantitative structure–activity relationship (QSAR) model based on bis- and ter-benzimidazoles, in an attempt to recognize the features that must be present in a molecule for it to behave as a topoisomerase I inhibitor. A data set comprising thirty bis-benzimidazoles and ter-benzimidazoles, known for their cytotoxicity against the RPMI-8402 lymphoblastoma cell line, has been chosen for this study. A five-point common pharmacophore hypothesis (CPH), with two acceptors, one donor and two aromatic features, has been derived for pharmacophore-based alignment of the molecules. The QSAR model, hence generated, shows a reasonable predictive Q2 value of 0.465. The CPH and contour map analyses display features that render antiproliferative properties to molecules against tumor cell lines, thereby ceasing cell growth. Further, the pharmacophore model has been utilized to develop lead molecules that can provide stability to the DNA–topoisomerase I cleavable complex, in turn inhibiting the activity of the enzyme. Virtual screening, followed by docking of obtained hits into the minor groove of B-DNA, gave three potent drugs, which are already approved drugs. The drug having the best fitness and binding score was further docked into the DNA–topoisomerase I cleavable complex. The present study opens up a new dimension in development of drugs for topoisomerase I inhibition.


Hoechst RPMI-8402 DNA–topoisomerase I Minor groove QSAR Virtual screening 



U.I. thanks the University Grants Commission (UGC), and R.A. and T.K. thank the Council of Scientific and Industrial Research (CSIR) for junior and senior research fellowships.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11224_2018_1257_MOESM1_ESM.doc (1.3 mb)
ESM 1 (DOC 1284 kb)


  1. 1.
    Castano IB, Brzoska PM, Sadoff BU, Chen H, Christman MF (1996) Mitotic chromosome condensation in the rDNA requires TRF4 and DNA topoisomerase I in Saccharomyces cerevisiae. Genes Dev 10:2564–2576PubMedGoogle Scholar
  2. 2.
    Lee MP, Brown SD, Chen A, Hsieh TS (1993) DNA topoisomerase I is essential in Drosophila melanogaster. Proc Natl Acad Sci U S A 90:6656–6660PubMedPubMedCentralGoogle Scholar
  3. 3.
    Morham SG, Kluckman KD, Voulomanos N, Smithies O (1996) Targeted disruption of the mouse topoisomerase I gene by camptothecin selection. Mol Cell Biol 16:6804–6809PubMedPubMedCentralGoogle Scholar
  4. 4.
    Wang JC (1996) DNA topoisomerases. Annu Rev Biochem 65:635–692PubMedGoogle Scholar
  5. 5.
    Zhang CX, Chen AD, Gettel NJ, Hsieh TS (2000) Essential functions of DNA topoisomerase I in Drosophila melanogaster. Dev Biol 222:27–40PubMedGoogle Scholar
  6. 6.
    Champoux JJ (2001) DNA topoisomerases: structure, function, and mechanism. Annu Rev Biochem 70:369–413PubMedGoogle Scholar
  7. 7.
    Champoux JJ (1990) Mechanistic aspects of type-I topoisomerases. In: Cozzarelli NR, Wang JC (eds) DNA topology and its biological effects, vol 20. Cold Spring Harbor Laboratory Press, Plainview, New York, pp 217–242Google Scholar
  8. 8.
    Wang JC (2002) Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 3:430–440PubMedPubMedCentralGoogle Scholar
  9. 9.
    Hertzberg RP, Hecht SM, Caranfa MJ (1989) On the mechanism of topoisomerase I inhibition by camptothecin: evidence for binding to an enzyme-DNA complex. Biochemistry 28:4629–4638PubMedGoogle Scholar
  10. 10.
    Hertzberg RP, Busby RW, Caranfa MJ, Holden KG, Johnson RK, Hecht SM, Kingsbury WD (1990) Irreversible trapping of the DNA-topoisomerase I covalent complex. Affinity labeling of the camptothecin binding site. J Biol Chem 265:19287–19295PubMedGoogle Scholar
  11. 11.
    Hsiang YH, Hertzberg RP, Hecht SM, Liu LF (1985) Camptothecin induces protein-linked DNA breaks via mammalian DNA topoisomerase I. J Biol Chem 260:14873–14878PubMedGoogle Scholar
  12. 12.
    Liu LF (1989) DNA topoisomerase poisons as antitumor drugs. Annu Rev Biochem 58:351–375PubMedGoogle Scholar
  13. 13.
    Liu LF, D’Arpa P (1992) Topoisomerase-targeting antitumor drugs: mechanisms of cytotoxicity and resistance. Important Adv Oncol 79–89Google Scholar
  14. 14.
    Pommier Y, Kohlhagen G, Kohn KW, Leteurtre F, Wani MC, Wall ME (1995) Interaction of an alkylating camptothecin derivative with a DNA base at topoisomerase I-DNA cleavage sites. Proc Natl Acad Sci U S A 92:8861–8865PubMedPubMedCentralGoogle Scholar
  15. 15.
    Porter SE, Champoux JJ (1989) The basis for camptothecin enhancement of DNA breakage by eukaryotic topoisomerase I. Nucleic Acids Res 17:8521–8532PubMedPubMedCentralGoogle Scholar
  16. 16.
    Potmesil M, Giovanella BC, Wall ME, Liu LF, Silber R, Stehlin JS, Wani MC, Hochster H (1993) Preclinical and clinical development of DNA topoisomerase I inhibitors in the United States. In: Andoh T, Ikeda H, Oguro M (eds) Molecular biology of DNA topoisomerases and its application to chemotherapy. CRC Press, Boca Raton, pp 301–311Google Scholar
  17. 17.
    Xu Z, Li T-K, Kim JS, LaVoie EJ, Breslauer KJ, Liu LF, Pilch DS (1998) DNA minor groove binding-directed poisoning of human DNA topoisomerase I by terbenzimidazoles. Biochemistry 37:3558–3566PubMedGoogle Scholar
  18. 18.
    Bailly C (2000) Topoisomerase I poisons and suppressors as anticancer drugs. Curr Med Chem 7:39–58PubMedGoogle Scholar
  19. 19.
    Pommier Y (1993) DNA topoisomerase I and II in cancer chemotherapy: update and perspectives. Cancer Chemother Pharmacol 32:103–108PubMedGoogle Scholar
  20. 20.
    Bansal S, Sinha D, Singh M, Cheng B, Tse-Dinh Y-C, Tandon V (2012) 3,4-Dimethoxyphenyl bis-benzimidazole, a novel DNA topoisomerase inhibitor that preferentially targets Escherichia coli topoisomerase I. J Antimicrob Chemother 67:2882–2891PubMedPubMedCentralGoogle Scholar
  21. 21.
    Ranjan N, Story S, Fulcrand G, Leng F, Ahmad M, King A, Sur S, Wang W, Tse-Dinh Y-C, Arya DP (2017) Selective inhibition of Escherichia coli RNA and DNA topoisomerase I by Hoechst 33258 derived mono- and bisbenzimidazoles. J Med Chem 60:4904–4922PubMedGoogle Scholar
  22. 22.
    Kim JS, Sun Q, Yu C, Liu A, Liu LF, LaVoie EJ (1998) Quantitative structure-activity relationships on 5-substituted terbenzimidazoles as topoisomerase I poisons and antitumor agents. Bioorg Med Chem 6:163–172PubMedGoogle Scholar
  23. 23.
    Mekapati SB, Hansch C (2001) Comparative QSAR studies on bibenzimidazoles and terbenzimidazoles inhibiting topoisomerase I. Bioorg Med Chem 9:2885–2893PubMedGoogle Scholar
  24. 24.
    Cramer RD, Patterson DE, Bunce JD (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110:5959–5967PubMedGoogle Scholar
  25. 25.
    Klebe G (1998) Comparative molecular similarity indices analysis, CoMSIA. Perspect Drug Disc Des 12:87–104Google Scholar
  26. 26.
    Winkler D (2011) Modelling topoisomerase I inhibition by minor groove binders. Bioorg Med Chem 19:1450–1457PubMedGoogle Scholar
  27. 27.
    Beerman TA, McHugh MM, Sigmund R, Lown JW, Rao KE, Bathini Y (1992) Effects of analogs of the DNA minor groove binder Hoechst 33258 on topoisomerase II and I mediated activities. Biochim Biophys Acta 1131:53–61PubMedGoogle Scholar
  28. 28.
    Chen AY, Chiang Y, Gatto B, Liu LF (1993) DNA minor groove-binding ligands: a different class of mammalian DNA topoisomerase I inhibitors. Proc Natl Acad Sci U S A 90:8131–8135PubMedPubMedCentralGoogle Scholar
  29. 29.
    Pilch DS, Xu Z, Sun Q, LaVoie EJ, Liu LF, Breslauer KJ (1997) A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: a potential mechanism for topoisomerase I poisoning. Proc Natl Acad Sci U S A 94:13565–13570PubMedPubMedCentralGoogle Scholar
  30. 30.
    Jin S, Kim JS, Sim S-P, Liu A, Pilch DS, Liu LF, LaVoie EJ (2000) Heterocyclic bibenzimidazole derivatives as topoisomerase I inhibitors. Bioorg Med Chem Lett 10:719–723PubMedGoogle Scholar
  31. 31.
    Kim JS, Gatto B, Yu C, Liu A, Liu LF, LaVoie EJ (1996) Substituted 2,5’-bi-1H-benzimidazoles: topoisomerase I inhibition and cytotoxicity. J Med Chem 39:992–998PubMedGoogle Scholar
  32. 32.
    Kim JS, Yu C, Liu A, Liu LF, LaVoie EJ (1997) Terbenzimidazoles: influence of 2″-, 4-, and 5-substituents on cytotoxicity and relative potency as topoisomerase I poisons. J Med Chem 40:2818–2824PubMedGoogle Scholar
  33. 33.
    Rangarajan M, Kim JS, Jin S, Sim S-P, Liu A, Pilch DS, Liu LF, LaVoie EJ (2000) 2″-Substituted 5-phenylterbenzimidazoles as topoisomerase I poisons. Bioorg Med Chem 8:1371–1382PubMedGoogle Scholar
  34. 34.
    Rangarajan M, Kim JS, Sim S-P, Liu A, Liu LF, LaVoie EJ (2000) Topoisomerase I inhibition and cytotoxicity of 5-bromo-and 5-phenylterbenzimidazoles. Bioorg Med Chem 8:2591–2600PubMedGoogle Scholar
  35. 35.
    Sun Q, Gatto B, Yu C, Liu A, Liu LF, LaVoie EJ (1994) Structure activity of topoisomerase I poisons related to Hoechst 33342. Bioorg Med Chem Lett 24:2871–2876Google Scholar
  36. 36.
    Sun Q, Gatto B, Yu C, Liu A, Liu LF, LaVoie EJ (1995) Synthesis and evaluation of terbenzimidazoles as topoisomerase I inhibitors. J Med Chem 38:3638–3644PubMedGoogle Scholar
  37. 37.
    Huang CC (1974) Cytogenetic study of human lymphoid T-cell lines derived from lymphocytic leukemia. J Natl Cancer Inst 53:655–660PubMedGoogle Scholar
  38. 38.
    Wold S, Ruhe A, Wold H, Dunn III WJ (1984) The collinearity problem in linear regression. The partial least squares (PLS) approach to generalized inverses. SIAM J Sci Stat Comp 5:735–743Google Scholar
  39. 39.
    Wold H (1985) Partial least squares. In: Kotz S, Johnson NL (eds) Encyclopedia of statistical sciences, vol 6. Wiley, New York, pp 581–591Google Scholar
  40. 40.
    Wold S, Johansson E, Cocchi M (1993) PLS-partial least squares projections to latent structures. In: Kubinyi H (ed) 3D QSAR in drug design: theory, method and applications. ESCOM Science Publishers, Leiden, pp 523–550Google Scholar
  41. 41.
    Dixon SL, Smondyrev AM, Rao SN (2006) PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chem Biol Drug Des 67:370–372PubMedGoogle Scholar
  42. 42.
    Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Freisner RA (2006) PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 20:647–671PubMedGoogle Scholar
  43. 43.
    Teng M-K, Usman N, Frederick CA, Wang AH-J (1988) The molecular structure of the complex of Hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG). Nucleic Acids Res 16:2671–2690PubMedPubMedCentralGoogle Scholar
  44. 44.
    Issar U, Kumari T, Arora R, Kakkar R (2017) Conformational properties of DNA minor groove binder Hoechst 33258 in gas phase and in aqueous solution. Comp Theo Chem 1113:32–41Google Scholar
  45. 45.
    Duffy EM, Jorgensen WL (2000) Prediction of properties from simulations: free energies of solvation in hexadecane, octanol, and water. J Am Chem Soc 122:2878–2888Google Scholar
  46. 46.
    Jorgensen WL, Duffy EM (2000) Prediction of drug solubility from Monte Carlo simulations. Bioorg Med Chem Lett 10:1155–1158PubMedGoogle Scholar
  47. 47.
    Issar U, Kumari T, Kakkar R (2015) Assessment of molecular binding of Hoechst 33258 analogues into DNA using docking and MM/GBSA approach. J Comp Sci 10:166–177Google Scholar
  48. 48.
    Kubinyi H (2008) Comparative molecular field analysis (CoMFA). In: Gasteiger J (ed) Handbook of chemoinformatics—from data to knowledge. Wiley-VCH Verlag GmbH, Weinheim, pp 1555–1574Google Scholar
  49. 49.
    Ray S (2012) QSAR modeling of antitmycobacterial activities of N-benzylsalicylamides and N-benzylsalicylthioamides derivatives against Mycobacterium kansasii CNCTC My (6509/96) using stepwise and PLS method. Int J ChemTech Res 4:41–47Google Scholar
  50. 50.
    Tenenhaus M, Vinzi VE, Chatelin Y-M, Lauro C (2005) PLS path modeling. Comp Stat Data Anal 48:159–205Google Scholar
  51. 51.
    Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shaw DE, Shelley M, Perry JK, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739–1749PubMedGoogle Scholar
  52. 52.
    Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein−ligand complexes. J Med Chem 49:6177–6196PubMedGoogle Scholar
  53. 53.
    Giménez BG, Santos MS, Ferrarini M, Fernandes JP (2010) Evaluation of blockbuster drugs under the rule-of-five. Pharmazie 65:148–152PubMedGoogle Scholar
  54. 54.
    Zhang MQ, Wilkinson B (2007) Drug discovery beyond the ‘rule-of-five’. Curr Opin Biotechnol 18:478–488PubMedGoogle Scholar
  55. 55.
    Matijević-Sosa J, Cvetnić Z (2005) Antimicrobial activity of N-phthaloylamino acid hydroxamates. Acta Pharma 55:387–399Google Scholar
  56. 56.
    Michot J-M, Seral C, van Bambeke F, Mingeot-Leclercq M-P, Tulkens PM (2005) Influence of efflux transporters on the accumulation and efflux of four quinolones (ciprofloxacin, levofloxacin, garenoxacin, and moxifloxacin) in J774 macrophages. Antimicrob Agents Chemother 49:2429–2437PubMedPubMedCentralGoogle Scholar
  57. 57.
    Vandenberg JI, Walker BD, Campbell TJ (2001) HERG K+ channels: friend and foe. Trends Pharmacol Sci 22:240–246PubMedGoogle Scholar
  58. 58.
    Aronov AM (2005) Predictive in silico modeling for hERG channel blockers. Drug Discov Today 10:149–155PubMedGoogle Scholar
  59. 59.
    Steinberg M (2007) Dasatinib: a tyrosine kinase inhibitor for the treatment of chronic myelogenous leukemia and Philadelphia chromosome-positive acute lymphoblastic leukemia. Clin Ther 29:2289–2308PubMedGoogle Scholar
  60. 60.
    Bellon S, Parsons JD, Wei Y, Hayakawa K, Swenson LL, Charifson PS, Lippke JA, Aldape R, Gross CH (2004) Crystal structures of Escherichia coli topoisomerase IV ParE subunit (24 and 43 kilodaltons): a single residue dictates differences in novobiocin potency against topoisomerase IV and DNA gyrase. Antimicrob Agents Chemother 48:1856–1864PubMedPubMedCentralGoogle Scholar
  61. 61.
    Burlison JA, Neckers L, Smith AB, Maxwell A, Blagg BS (2006) Novobiocin: redesigning a DNA gyrase inhibitor for selective inhibition of hsp90. J Am Chem Soc 128:15529–15536PubMedGoogle Scholar
  62. 62.
    Lanoot B, Vancanneyt M, Cleenwerck I, Wang L, Li W, Liu Z, Swings J (2002) The search for synonyms among streptomycetes by using SDS-PAGE of whole-cell proteins. Emendation of the species Streptomyces aurantiacus, Streptomyces cacaoi subsp. cacaoi, Streptomyces caeruleus and Streptomyces violaceus. Int J SysT Evol Microbiol 52:823–829PubMedGoogle Scholar
  63. 63.
    Burris IIIHA (2004) Dual kinase inhibition in the treatment of breast cancer: initial experience with the EGFR/ErbB-2 inhibitor lapatinib. Oncologist 3:10–15Google Scholar
  64. 64.
    Higa GM, Abraham J (2007) Lapatinib in the treatment of breast cancer. Future Drugs 7:1183–1192Google Scholar
  65. 65.
    Rusnak DW, Lackey K, Affleck K, Wood ER, Alligood KJ, Rhodes N, Keith BR, Murray DM, Knight WB, Mullin RJ, Gilmer TM (2001) The effects of the novel, reversible epidermal growth factor receptor/ErbB-2 tyrosine kinase inhibitor, GW2016, on the growth of human normal and tumor-derived cell lines in vitro and in vivo. Mol Cancer Ther 1:85–94PubMedGoogle Scholar
  66. 66.
    Stewart LM, Redinbo MR, Qiu XY, Hol WG, Champoux JJ (1998) A model for the mechanism of human topoisomerase I. Science 279(5356):1534–1541PubMedGoogle Scholar
  67. 67.
    Khan QA, Pilch DS (2007) Topoisomerase I-mediated DNA cleavage induced by the minor groove-directed binding of bibenzimidazoles to a distal site. J Mol Biol 365:561–569PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Upasana Issar
    • 1
  • Richa Arora
    • 1
  • Tripti Kumari
    • 1
  • Rita Kakkar
    • 1
    Email author
  1. 1.Computational Chemistry Laboratory, Department of ChemistryUniversity of DelhiDelhiIndia

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