Human Topoisomerase I Inhibitors


Topoisomerases are ubiquitous enzymes that solve topological problems due to DNA (deoxyribonucleic acid) supercoiling occurring during the replication, transcription, recombination and chromatin remodelling processes. Human topoisomerase IB (Topo IB) is the selective target of camptothecin, a natural compound from which two powerful anticancer drugs, topotecan and irinotecan, are produced. Camptothecin acts as an interfacial inhibitor interacting with both the enzyme and DNA stabilising the covalent enzyme–DNA complex, and slowing down the religation of the broken DNA strands brings cells to death. Topo IB is also important for transcription of genes involved in neurodevelopment, and its inhibition during critical stages of brain development may be responsible for neurodevelopmental disorders.

Key Concepts

  • Topoisomerases are crucial enzymes essential in the relaxation of supercoiled DNA.
  • Human topoisomerase IB cuts a single DNA strand forming a transient enzyme–DNA cleavage complex.
  • Camptothecin is a natural compound of which human topoisomerase IB is the only cellular target.
  • Camptothecin can trap the enzyme–DNA cleavage complex bringing cells to death.
  • Two camptothecin derivatives have been approved by the US Food and Drug Administration: topotecan for ovarian and lung cancers and irinotecan for colorectal cancer.
  • Camptothecin and its derivatives act as interfacial inhibitors interacting with both the enzyme and the DNA.
  • Single topoisomerase mutation may induce resistance to camptothecin.
  • New non‐camptothecin derivatives are under development.
  • The cytotoxic activity of camptothecin increases in the presence of other compounds inhibiting enzymes involved in DNA repair.
  • Inhibition of topoisomerase IB has also a strong influence on the modulation expression of groups of genes associated with autism.

Keywords: topoisomerase; supercoiled DNA; camptothecin; anticancer drugs; neurodevelopmental disorders

Figure 1. Scheme of the DNA cleavage reaction from topoisomerase IB highlighting the formation of the DNA–enzyme cleavage complex. The detail of the covalent bond between tyrosine 723 and the 3′ end of the strand is also highlighted.
Figure 2. (a) Scheme of the topoisomerase IB sequence representing the domains in different colours (white: N‐terminal; yellow, blue and red: core domain, green: linker domain). The core domain is subdivided into subdomain 1: yellow, subdomain 2: blue and subdomain 3: red. The five residues forming the catalytic pentad are represented by stars with tyrosine 732, undergoing the nucleophilic attack, represented by a black star. (b) 3D structure of topoisomerase in covalent complex with a linear DNA double strand. The colour code is the same as that of the sequence.
Figure 3. Scheme of the catalytic cycle of the Topo I enzyme, showing the different steps required to relax a supercoiled DNA substrate.
Figure 4. Chemical formula of the active and inactive forms of camptothecin (a); of topotecan and SN38 (b) and of some derivatives representing the indenoisoquinolines family (c).
Figure 5. 3D structure of the ternary Topo I–DNA–topotecan complex. In the upper part the stacking of the drug with the DNA bases at the nicked site is highlighted; in the lower part the protein–drug hydrogen bonds are highlighted.


Albor A, Kaku S and Kulesz‐Martin M (1998) Cancer Research 58: 2091–2094.

Antony S, Jayaraman M, Laco G, et al. (2003) Differential induction of topoisomerase I‐DNA cleavage complexes by the indenoisoquinoline MJ‐III‐65 (NSC 706744) and camptothecin. Cancer Research 63: 7428–7435.

Bain AL, Mastrocola AS, Tibbetts RS and Khanna KK (2014) DNA damage response: from tumourigenesis to therapy. In: eLS. Chichester: John Wiley & Sons Ltd.; doi:10.1002/9780470015902.a0006107.pub2.

Bowater RP (2015) Supercoiled DNA: structure. In: eLS. Chichester: John Wiley & Sons Ltd.; doi:10.1002/9780470015902.a0001040.pub3.

Bruzzese F, Rocco M, Castelli S, et al. (2009) Synergistic antitumor effect between vorinostat and topotecan in small cell lung cancer cells is mediated by generation of reactive oxygen species and DNA damage‐induced apoptosis. Molecular Cancer Therapeutics 8 (11): 3075–3087.

Castelli S, Katkar P, Vassallo O, et al. (2012) A natural anticancer agent thaspine targets human topoisomerase IB. Anticancer Agents Medicinal Chemistry 13 (2): 356–363.

Chillemi G, Fiorani P, Castelli S, et al. (2005) Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I: a functional and molecular dynamics study. Nucleic Acids Research 33: 3339–3350.

Chillemi G, D'Annessa I, Fiorani P, et al. (2008) Thr729 in human topoisomerase I modulates anti‐cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations. Nucleic Acids Research 36: 5645–5651.

Coletta A and Desideri A (2013) Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study. Nucleic Acids Research 41 (22): 9977–9986.

Covey JM, Jaxel C, Kohn KW and Pommier Y (1989) Protein‐linked DNA strand breaks induced in Mammalian cells by camptothecin, an inhibitor of topoisomerase I. Cancer Research 49: 5016–5022.

Chrencik JE, Staker BL, Burgin AB, et al. (2004) Mechanisms of camptothecin resistance by human topoisomerase I mutations. Journal of Molecular Biology 339 (4): 773–784.

D'Annessa I, Coletta A, Sutthibutpong T, et al. (2014) Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein–DNA binding site. Nucleic Acids Research 42 (14): 9304–9312.

Eng WK, Faucette L, Johnson RK and Sternglanz R (1988) Evidence that DNA topoisomerase I is necessary for the cytotoxic effects of camptothecin. Molecular Pharmacology 34: 755–760.

Fayad W, Fryknäs M, Brnjic S, et al. (2009) Identification of a novel topoisomerase inhibitor effective in cells overexpressing drug efflux transporters. PLoS One 4: e7238.

Fiorani P, Bruselles A, Falconi M, et al. (2003) Single mutation in the linker domain confers flexibility and camptothecin resistance to human topoisomerase I. Journal of Biological Chemistry 278: 43268–43275.

Fiorani P, Chillemi G, Losasso C, Castelli S and Desideri A (2006) The different cleavage DNA sequence specificity explains the camptothecin resistance of the human topoisomerase I Glu418Lys mutant. Nucleic Acids Research 34: 5093–5100.

Fiorani P, Tesauro C, Mancini G, et al. (2009) Evidence of the crucial role of the linker domain on the catalytic activity of human topoisomerase I by experimental and simulative characterization of the Lys681Ala mutant. Nucleic Acids Research 37: 6849–6858.

Gatto B, Sanders MM, Yu C, et al. (1996) Identification of topoisomerase I as the cytotoxic target of the protoberberine alkaloid coralyne. Cancer Research 56: 2795–2800.

Gongora C, Vezzio‐Vie N, Tuduri S, et al. (2011) New topoisomerase I mutations are associated with resistance tocamptothecin. Molecular Cancer 10: 64.

Horwitz SB (1975) Antibiotics. In: Corcoran JW and Hahn FE (eds) Mechanism of Action of Antimicrobial and Antitumor Agents, vol. 111, pp. 48–57. New York: Springer‐Verlag.

Hsiang YH, Hertzberg R, Hecht S and Liu LF (1985) Camptothecin induces protein‐linked DNA breaks via mammalian DNA topoisomerase I. Journal of Biological Chemistry 260: 14873–14878.

Jaxel C, Capranico G, Kerrigan D, Kohn KW and Pommier Y (1991) Effect of local DNA sequence on topoisomerase I cleavage in the presence or absence of camptothecin. Journal of Biological Chemistry 266: 20418–20423.

King IF, Yandava CN, Mabb AM, et al. (2013) Topoisomerases facilitate transcription of long genes linked toautism. Nature 501 (7465): 58–62.

Limpose K, Corbett AH and Doetsch PW (2014) DNA damage. In: eLS. Chichester: John Wiley & Sons Ltd.; doi:10.1002/9780470015902.a0000557.pub3.

Lv PC, Agama K, Marchand C, Pommier Y and Cushman M (2014) Synthesis, and biological evaluation of O‐2‐modified indenoisoquinolines as dual topoisomerase I‐tyrosyl‐DNA phosphodiesterase I inhibitors. Journal of Medicinal Chemistry 57 (10): 4324–4336.

Mabb AM, Kullmann PH, Twomey MA, et al. (2014) Topoisomerase 1 inhibition reversibly impairs synaptic function. Proceedings of the National Academy of Sciences of the United States of America 111 (48): 17290–17295.

Makeyev Y, Muggia FM, Rajan A, et al. (2012) Topoisemerase I inhibitors In: Pommier Y (ed.) DNA Topoisomerases and Cancer. New York: Springer, pp. 245–277.

Madden KR, Stewart L and Champoux JJ (1995) Preferential binding of human topoisomerase I to superhelical DNA. EMBO Journal 14: 5399–5409.

Mancini G, D'Annessa I, Coletta A, et al. (2010) Structural and dynamical effects induced by the anticancer drug topotecan on the human topoisomerase I ‐ DNA complex. PLoS One 5: e10934.

Mancini G, D'Annessa I, Coletta A, et al. (2012) Binding of an Indenoisoquinoline to the topoisomerase‐DNA complex induces reduction of linker mobility and strengthening of protein‐DNA interaction. PLoS One 7: e51354.

Merino A, Madden KR, Lane WS, Champoux JJ and Reinberg D (1993) Nature 365: 227–232.

Miao ZH, Player A, Shankavaram U, et al. (2007) Nonclassic functions of human topoisomerase I: genome‐wide and pharmacologic analyses. Cancer Research 67: 8752–8761.

Misteli T (2007) Beyond the sequence: cellular organization of genome function. Cell 128 (4): 787–800.

Nguyen TX, Morrell A, Conda‐Sheridan M, et al. (2012) Synthesis and biological evaluation of the first dual tyrosyl‐DNA phosphodiesterase I (Tdp1)‐topoisomerase I (Top1) inhibitors. Journal of Medicinal Chemistry 55 (9): 4457–4478.

Nguyen TX, Abdelmalak M, Marchand C, Pommier Y and Cushman M (2015) Synthesis and biological evaluation of nitrated 7‐, 8‐, 9‐, and 10‐hydroxyindenoisoquinolines as potential dual topoisomerase I (Top1)–tyrosyl‐DNA phosphodiesterase I (TDP1) inhibitors. Journal of Medicinal Chemistry 58 (7): 3188–3208.

Nitiss J and Wang JC (1988) DNA topoisomerase‐targeting antitumor drugs can be studied in yeast. Proceedings of the National Academy of Sciences of the United States of America 85: 7501–7505.

Pakotiprapha D and Jeruzalmi D (2014) Crystallization of protein–DNA complexes. In: eLS. Chichester: John Wiley & Sons Ltd.; doi: 10.1002/9780470015902.a0002720.pub3.

Pommier Y, Leo E, Zhang H and Marchand C (2010) DNA topoisomerases and their poisoning by anticancer and antibacterial drugs. Chemistry & Biology 17 (5): 421–433.

Pommier Y (2013) Drugging topoisomerases: lessons and challenges. ACS Chemical Biology. 8 (1): 82–95.

Redinbo MR, Stewart L, Kuhn P, Champoux JJ and Hol WGJ (1998) Crystal structures of human topoisomerase I in covalent and non‐covalent complexes with DNA. Science 279: 1504–1513.

Sirikantaramas S, Yamazaki M and Saito K (2008) Mutations in topoisomerase I as a self‐resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants. Proceedings of the National Academy of Sciences of the United States of America 105: 6782–6786.

Smith SJ, Li CM, Hickey RJ and Malkas LH (2014) DNA replication: mammalian. In: eLS. Chichester: John Wiley & Sons Ltd.; doi:10.1002/9780470015902.a0001041.pub3.

Staker BL, Hjerrild K, Feese MD, et al. (2002) The mechanism of topoisomerase I poisoning by a camptothecin analog. Proceedings of the National Academy of Sciences of the United States of America 99: 15387–15392.

Staker BL, Feese MD, Cushman M, et al. (2005) Structures of three classes of anticancer agents bound to the human topoisomerase I‐DNA covalent complex. Journal of Medicinal Chemistry 48: 2336–2345.

Stewart L, Ireton GC, Parker LH, Madden KR and Champoux JJ (1996) Journal of Biological Chemistry 271: 7593–7601.

Stewart L, Redinbo MR, Qiu X, Hol WGJ and Champoux JJ (1998) A model for the mechanism of human topoisomerase I. Science 279: 1534–1541.

Stewart L, Ireton GC and Champoux JJ (1999) A functional linker in human topoisomerase I is required for maximum sensitivity to camptothecin in a DNA relaxation assay. Journal of Biological Chemistry 274: 32950–32960.

Subramanian D, Kraut E, Staubus A, Young DC and Muller MT (1995) Analysis of topoisomerase I/DNA complexes in patients administered topotecan. Cancer Research 55: 2097–2103.

Tesauro C, Fiorani P, D'Annessa I, et al. (2010) Erybraedin C, a natural compound from the plant Bituminaria bituminosa, inhibits both the cleavage and religation activities of human topoisomerase I. Biochemical Journal 425 (3): 531–539.

Tesauro C, Morozzo della Rocca B, Ottaviani A, et al. (2013) Molecular mechanism of the camptothecin resistance of Glu710Gly topoisomerase IB mutant analyzed in vitro and in silico. Molecular Cancer 12 (100): 1–13.

Vassallo O, Castelli S, D'Annessa I, et al. (2011) Evidences of a natively unfolded state for the human topoisomerase IB N‐terminal domain. Amino Acids 41 (4): 945–953.

Wang JC (2002) Cellular roles of DNA topoisomerases: a molecular perspective. Nature Review Molecular Cellular Biology 3: 430–440.

Wang LK, Johnson RK and Hecht SM (1993) Inhibition of topoisomerase I function by nitidine and fagaronine. Chemical Research in Toxicology 6: 813–818.

Yang SW, Burgin AB Jr, Huizenga BN, et al. (1996) A eukaryotic enzyme that can disjoin dead‐end covalent complexes between DNA and type I topoisomerases. Proceedings of the National Academy of Sciences of the United States of America 93 (21): 11534–11539.

Further Reading

Beretta GL, Gatti L, Perego P and Zaffaroni N (2013) Camptothecin resistance in cancer: insights into the molecular mechanisms of a DNA‐damaging drug. Current Medicinal Chemistry 20 (12): 1541–1565.

Castelli S, Coletta A, D'Annessa I, et al. (2012) Interaction between natural compounds and human topoisomerase. Biological Chemistry 393 (11): 1327–1340.

D'Annessa I, Castelli S and Desideri A (2015) Topoisomerase 1B as a target against leishmaniasis. Mini Review Medicinal Chemistry 15 (3): 203–210.

Kümler I, Brünner N, Stenvang J, Balslev E and Nielsen DL (2013) A systematic review on topoisomerase 1 inhibition in the treatment of metastatic breast cancer. Breast Cancer Research and Treatment 138 (2): 347–358.

Pommier Y (2006) Topoisomerase I inhibitors: camptothecins and beyond. Nature Review Cancer 6 (10): 789–802.

Pommier Y (2009) DNA topoisomerase I inhibitors: chemistry, biology and interfacial inhibition. Chemical reviews 109 (7): 2894–2902.

Vokálová L, Durdiaková J and Ostatníková D (2015) Topoisomerases interlink genetic network underlying autism. International Journal of Developmental Neuroscience 47: 361–368.

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Desideri, Alessandro(Aug 2016) Human Topoisomerase I Inhibitors. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0026795]