Abstract
Aim: The previously reported dual histone deacetylase type II (HDAC II) / topoisomerase type I (Topo I) inhibitors suffer pharmacokinetic limitations because of their huge molecular weights. Materials & methods: We report the design and synthesis of a smarter novel set of uracil-linked Schiff bases (19–30) as dual HDAC II/Topo I inhibitors keeping the essential pharmacophoric features. Cytotoxicity of all compounds was assessed against three cancer cell lines. Studies of their effects on the apoptotic BAX and antiapoptotic BCL2 genes, molecular docking studies, and absorption, distribution, metabolism and excretion studies were conducted. Results: Compounds 22, 25 and 30 exhibited significant activities. The bromophenyl derivative 22 displayed the best selectivity index, with IC50 values against HDAC II and Topo I of 1.12 and 13.44 μM, respectively. Conclusion: Compound 22 could be considered a lead HDAC II/Topo I inhibitor.
Graphical abstract
Papers of special note have been highlighted as: • of interest
References
- 1. American Cancer Society. Cancer facts and figures 2022 (2023). www.cancer.org/research/cancer-facts-statistics/all-cancer-facts-figures/cancer-facts-figures-2022.html#:∼:text=Estimatednumbersofnewcancer,incidence%2Cmortality%2Candsurvivalstatistics
- 2. . A view on drug resistance in cancer. Nature 575(7782), 299–309 (2019).
- 3. . New quinoxalin-2(1H)-one-derived VEGFR-2 inhibitors: design, synthesis, in vitro anticancer evaluations, in silico ADMET, and docking studies. Arch. Pharm. 355(7), e2200048 (2022).
- 4. Ligand-based design on the dog-bone-shaped BIBR1532 pharmacophoric features and synthesis of novel analogues as promising telomerase inhibitors with in vitro and in vivo evaluations. J. Med. Chem. 66(1), 777–792 (2023).
- 5. . Dual inhibitors of human DNA topoisomerase II and other cancer-related targets. J. Med. Chem. 63(3), 884–904 (2020). • Describes the benefits of using medications with dual targets to manage chemotherapeutics-resistant cancers.
- 6. Rational design of multitarget-directed ligands: strategies and emerging paradigms. J. Med. Chem. 62(20),8881–8914 (2019).
- 7. . Protein tyrosine kinase inhibitor resistance in malignant tumors: molecular mechanisms and future perspective. Signal Transduct. Target. Ther. 7(1), 329 (2022).
- 8. . A definition of ‘multitargeticity’: identifying potential multitarget and selective ligands through a vector analysis. Front. Chem. 8, 176 (2020).
- 9. . Multi-target pharmacology: possibilities and limitations of the ‘skeleton key approach’ from a medicinal chemist perspective. Front. Pharmacol. 6, 205 (2015)
- 10. . The multitarget approach as a green tool in medicinal chemistry. In: Contemporary Chemical Approaches for Green and Sustainable Drugs. Elsevier, Amsterdam, The Netherlands, 457–492 (2022).
- 11. . Polypharmacology in a single drug: multitarget drugs. Curr. Med. Chem. 20(13), 1639–1645 (2013).
- 12. . From single- to multi-target drugs in cancer therapy: when aspecificity becomes an advantage. Curr. Med. Chem. 15(5), 422–432 (2008).
- 13. . Extended multitarget pharmacology of anticancer drugs. J. Chem. Inf. Model. 59(6), 3006–3017 (2019).
- 14. . Anti-angiogenic tyrosine kinase inhibitors: what is their mechanism of action? Angiogenesis 13(1), 1–14 (2010).
- 15. . N-Substituted-4-phenylphthalazin-1-amine-derived VEGFR-2 inhibitors: design, synthesis, molecular docking, and anticancer evaluation studies. Arch. Pharm. 354(3), e202000219 (2021).
- 16. Design, synthesis, molecular docking, anticancer evaluations, and in silico pharmacokinetic studies of novel 5-[(4-chloro/2,4-dichloro)benzylidene]thiazolidine-2,4-dione derivatives as VEGFR-2 inhibitors. Arch. Pharm. 354(2), e2000279 (2021).
- 17. . Design, synthesis, docking, ADMET profile, and anticancer evaluations of novel thiazolidine-2,4-dione derivatives as VEGFR-2 inhibitors. Arch. Pharm. 354(7), e2000491 (2021).
- 18. 1,2,4-Triazolo[4,3-c]quinazolines: a bioisosterism-guided approach towards the development of novel PCAF inhibitors with potential anticancer activity. New J. Chem. 45(25), 11136–11152 (2021).
- 19. . Novel triazolophthalazine-hydrazone hybrids as potential PCAF inhibitors: design, synthesis, in vitro anticancer evaluation, apoptosis, and molecular docking studies. Bioorg. Chem. 100, 103899 (2020).
- 20. . Design, synthesis, and antitumor activity of novel compounds based on 1,2,4-triazolophthalazine scaffold: apoptosis-inductive and PCAF-inhibitory effects. Bioorg. Chem. 101, 104019 (2020).
- 21. . Dual targeting of histone deacetylase and topoisomerase II with novel bifunctional inhibitors. J. Med. Chem. 55(4), 1465–1477 (2012).
- 22. . A novel anti-cancer bifunctional platinum drug candidate with dual DNA binding and histone deacetylase inhibitory activity. Chem. Commun. (44), 6735–6737 (2009). https://pubs.rsc.org/en/content/articlelanding/2009/cc/b916715c/unauth
- 23. . Roles of eukaryotic topoisomerases in transcription, replication and genomic stability. Nat. Rev. Mol. Cell Biol. 17(11), 703–721 (2016).
- 24. Subcellular localization of class I histone deacetylases in the developing Xenopus tectum. Front. Cell. Neurosci. 9, 510 (2016).
- 25. Discovery of novel multiacting topoisomerase I/II and histone deacetylase inhibitors. ACS Med. Chem. Lett. 6(3), 239–243 (2015).
- 26. . Dual-acting histone deacetylase–topoisomerase I inhibitors. Bioorg. Med. Chem. Lett. 23(11), 3283–3287 (2013).
- 27. The discovery and optimization of novel dual inhibitors of topoisomerase II and histone deacetylase. Bioorg. Med. Chem. 21(22), 6981–6995 (2013). • Shows the the utilization of 5-fluorouracil as a key pharmacophore in the structures of structure with reported histone deacetylase (HDAC) and topoisomerase (Topo) inhibitors.
- 28. Hybrid topoisomerase I and HDAC inhibitors as dual action anticancer agents. PLOS ONE 13(10), e0205018 (2018). • Reports the synergistic anticancer effect upon a concurrent treatment with Topo I/HDAC II dual inhibitor medications.
- 29. . The FDA-approved anti-cancer drugs, streptozotocin and floxuridine, reduce the virulence of Staphylococcus aureus. Sci. Rep. 8(1), 2521 (2018).
- 30. Identification of FDA-approved oncology drugs with selective potency in high-risk childhood ependymoma. Mol. Cancer Ther. 17(9), 1984–1994 (2018).
- 31. Identification of 2(1H)-pyrimidinones as potential EGFR T790M inhibitors for the treatment of gefitinib-resistant non-small cell lung cancer. Bioorg. Chem. 89, 102994 (2019).
- 32. Utilization of tetrahydrobenzo[4,5]thieno[2,3-d]pyrimidinone as a cap moiety in design of novel histone deacetylase inhibitors. Bioorg. Chem. 91, 103127 (2019).
- 33. . Synthesis, anticancer activity and molecular docking study of Schiff base complexes containing thiazole moiety. Beni-Suef Univ. J. Basic Appl. Sci. 5(1), 85–96 (2016).
- 34. . Synthesis and molecular docking studies of some novel Schiff bases incorporating 6-butylquinolinedione moiety as potential topoisomerase IIβ inhibitors. R. Soc. Open Sci. 5(6), 172407 (2018).
- 35. Schiff bases as linker in the development of quinoline-sulfonamide hybrids as selective cancer-associated carbonic anhydrase isoforms IX/XII inhibitors: a new regioisomerism tactic. Bioorg. Chem. 131, 106309 (2023).
- 36. A novel small molecule hybrid of vorinostat and DACA displays anticancer activity against human hormone-refractory metastatic prostate cancer through dual inhibition of histone deacetylase and topoisomerase I. Biochem. Pharmacol. 90(3), 320–330 (2014). • Reports the synergistic anticancer effect upon a concurrent treatment with Topo I/HDAC II dual inhibitor medications.
- 37. . Polypharmacology by design: a medicinal chemist’s perspective on multitargeting compounds. J. Med. Chem. 62(2), 420–444 (2019).
- 38. . Design and synthesis of novel camptothecin/5-fluorouracil conjugates as cytotoxic agents. Nat. Prod. Res. 25(19), 1817–1826 (2011).
- 39. . Development of novel anticancer agents with a scaffold of tetrahydropyrido [4, 3-d] pyrimidine-2, 4-dione. ACS Med. Chem. Lett. 10(2), 191–195 (2019).
- 40. . Design, synthesis and biological evaluation of novel uracil derivatives bearing 1,2,3-triazole moiety as thymidylate synthase (TS) inhibitors and as potential antitumor drugs. Eur. J. Med. Chem. 171, 282–296 (2019).
- 41. Design, synthesis, and molecular docking studies of new [1,2,4]triazolo[4,3-a]quinoxaline derivatives as potential A2B receptor antagonists. Mol. Divers. 25(1), 291–306 (2021).
- 42. . Synthesis and evaluation of some new (1,2,4) triazolo(4,3-a)quinoxalin-4(5h)-one derivatives as AMPA receptor antagonists. J. Heterocycl. Chem. 50(5), 1202–1208 (2013).
- 43. In vivo- and in silico-driven identification of novel synthetic quinoxalines as anticonvulsants and AMPA inhibitors. Arch. Pharm. 354(5), e2000449 (2021).
- 44. In vitro and computational investigations of novel synthetic carboxamide-linked pyridopyrrolopyrimidines with potent activity as SARS-CoV-2-M Pro inhibitors. RSC Adv. 12(41), 26895–26907 (2022).
- 45. . Rationale design, synthesis, cytotoxicity evaluation, and in silico mechanistic studies of novel 1,2,3-triazoles with potential anticancer activity. New J. Chem. 46, 12206–12216 (2022).
- 46. . The effect of novel synthetic semicarbazone- and thiosemicarbazone-linked 1,2,3-triazoles on the apoptotic markers, VEGFR-2, and cell cycle of myeloid leukemia. Bioorg. Chem. 127, 105968 (2022).
- 47. . Exploring the cytotoxic effect and CDK-9 inhibition potential of novel sulfaguanidine-based azopyrazolidine-3,5-diones and 3,5-diaminoazopyrazoles. Bioorg. Chem. 133, 106397 (2023).
- 48. Downregulation of HDAC6 promotes angiogenesis in hepatocellular carcinoma cells and predicts poor prognosis in liver transplantation patients. Mol. Carcinog. 55(5), 1024–1033 (2016).
- 49. . Combination of HDAC and topoisomerase inhibitors in small cell lung cancer. Cancer Biol. Ther. 13(8), 614–622 (2012).
- 50. . Targeting histone modifications in breast cancer: a precise weapon on the way. Front. Cell Dev. Biol. 9, 736935 (2021).
- 51. . Synthesis, DNA binding and antiviral activity of new uracil, xanthine, and pteridine derivatives. Arch. Pharm. 340(1), 26–31 (2007). • Reports the synthetic procedure of 5,6-diamino-1,3-dimethyluracil hydrochloride (17a).
- 52. . One pot synthesis, DNA binding and fragmentation in vitro of new fused uracil derivatives for anticancer properties. Afinidad 69(559), 224–228 (2012). • Reports the synthetic procedure of 5,6-diamino-1,3-dimethyluracil hydrochloride (17a).
- 53. . Novel uracil derivatives depicted potential anticancer agents: in vitro, molecular docking, and ADME study. Arab. J. Chem. 15(4), 103669 (2022).
- 54. . Synthesis, molecular docking and anticancer activity of some 5-aryl-5, 10-dihydropyrido [2, 3-d: 6, 5-d′] dipyrimidine-2, 4, 6, 8-tetraone derivatives and pyrido [2, 3-d] pyrimidines. ChemistrySelect 7(7), e202103834 (2022).
- 55. . Synthesis, in silico prediction and in vitro evaluation of antimicrobial activity, dft calculation and theoretical investigation of novel xanthines and uracil containing imidazolone derivatives. Int. J. Mol. Sci. 22(20), 10979 (2021).
- 56. . Synthesis, in silico prediction and in vitro evaluation of antitumor activities of novel pyrido [2,3-d] pyrimidine, xanthine and lumazine derivatives. Molecules 25(21), 5205 (2020).
- 57. One-pot synthesis and molecular modeling studies of new bioactive spiro-oxindoles based on uracil derivatives as SARS-CoV-2 inhibitors targeting RNA polymerase and spike glycoprotein. Pharmaceuticals 15(3), 376 (2022).
- 58. . Uracil as a Zn-binding bioisostere of the allergic benzenesulfonamide in the design of quinoline–uracil hybrids as anticancer carbonic anhydrase inhibitors. Pharmaceuticals 15(5), 494 (2022).
- 59. . Use of an aqueous soluble tetrazolium/formazan assay for cell growth assays in culture. Cancer Commun. 3(7), 207–212 (1991).
- 60. Chemical phylogenetics of histone deacetylases. Nat. Chem. Biol. 6(3), 238–243 (2010).
- 61. . Bistratamides M and N, oxazole-thiazole containing cyclic hexapeptides isolated from Lissoclinum bistratum interaction of zinc(II) with bistratamide K. Mar. Drugs 15(7), 209 (2017).
- 62. . A novel assay for apoptosis. Flow cytometric detection of phosphatidylserine expression on early apoptotic cells using fluorescein labelled annexin V. J. Immunol. Methods 184(1), 39–51 (1995).
- 63. . Assaying cell cycle status using flow cytometry. Curr. Protoc. Mol. Biol. 111(1), 28.6.1–28.6.11 (2015).
- 64. Chemical Computing Group, Inc. Molecular Operating Environment (MOE 2019.0102). https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=+Molecular+Operating+Environment+%28MOE+2019.0102%29&btnG=
- 65. Anticoagulants as potential SARS-CoV-2 Mpro inhibitors for COVID-19 patients: in vitro, molecular docking, molecular dynamics, DFT, and SAR studies. Int. J. Mol. Sci. 23(20), 12235 (2022).
- 66. . SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. 7(1), 42717 (2017).
- 67. . Phthalazine-based VEGFR-2 inhibitors: rationale, design, synthesis, in silico, ADMET profile, docking, and anticancer evaluations. Arch. Pharm. 354(11), e2100201 (2021).
- 68. . Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. J. Immunol. Methods 65(1–2), 55–63 (1983).
- 69. Cytotoxic effect of a novel naphthylchalcone against multiple cancer cells focusing on hematologic malignancies. Biochimie 140, 48–57 (2017).
- 70. . DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70(1), 369–413 (2001).
- 71. . Structural studies of type I topoisomerases. Nucleic Acids Res. 37(3), 693–701 (2009).
- 72. . Apoptosis: a review of programmed cell death. Toxicol. Pathol. 35(4), 495–516 (2007).
- 73. . Apoptosis induction, PARP-1 inhibition, and cell cycle analysis of leukemia cancer cells treated with novel synthetic 1,2,3-triazole-chalcone conjugates. Bioorg. Chem. 123, 105762 (2022).
- 74. . Apoptosis and molecular targeting therapy in cancer. Biomed Res. Int. 2014, 1–23 (2014).
- 75. . Centrosome-associated regulators of the G2/M checkpoint as targets for cancer therapy. Mol. Cancer 8(1), 8 (2009).
- 76. . Expression of p53 protein and the apoptotic regulatory molecules Bcl-2, Bcl-XL, and Bax in locally advanced squamous cell carcinoma of the lung. Lung Cancer 45(2), 181–188 (2004).
- 77. Bcl-2/Bax protein ratio predicts 5-fluorouracil sensitivity independently of p53 status. Br. J. Cancer 83(10), 1380–1386 (2000).
- 78. Synthesis, structural characterization, DFT calculations, molecular docking, and molecular dynamics simulations of a novel ferrocene derivative to unravel its potential antitumor activity. J. Biomol. Struct. Dyn. 1–18.
doi: 10.1080/07391102.2022.2082533 (2022) (Epub ahead of print). - 79. . The mechanism of topoisomerase I poisoning by a camptothecin analog. Proc. Natl Acad. Sci. USA 99(24), 15387–15392 (2002).
- 80. . Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23(1–3), 3–25 (1997).
- 81. . Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 45(12), 2615–2623 (2002).
- 82. . A new atom-additive method for calculating partition coefficients. J. Chem. Inf. Comput. Sci. 37(3), 615–621 (1997).
- 83. . A BOILED-Egg to predict gastrointestinal absorption and brain penetration of small molecules. ChemMedChem 11(11), 1117–1121 (2016).
- 84. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin. 71(3), 209–249 (2021).