Identification of dual binding mode of Orthodiffenes towards human topoisomerase-I and α-tubulin: exploring the potential role in anti-cancer activity via in silico study

Reference

• Antolin, A. A., Workman, P., Mestres, J., & Al-Lazikani, B. (2016). Polypharmacology in precision oncology: Current applications and future prospects. Current Pharmaceutical Design, 22(46), 6935–6945.https://doi.org/10.2174/1381612822666160923
   PubMed Web of Science ®Google Scholar
• Araújo, P. H. F., Ramos, R. S., da Cruz, J. N., Silva, S. G., Ferreira, E. F. B., de Lima, L. R., Macêdo, W. J. C., Espejo-Román, J. M., Campos, J. M., & Santos, C. B. R. (2020). Identification of potential COX-2 inhibitors for the treatment of inflammatory diseases using molecular modeling approaches. Molecules, 25(18), 4183. https://doi.org/10.3390/molecules25184183
   PubMed Web of Science ®Google Scholar
• Bennion, B. J., Be, N. A., McNerney, M. W., Lao, V., Carlson, E. M., Valdez, C. A., Malfatti, M. A., Enright, H. A., Nguyen, T. H., Lightstone, F. C., & Carpenter, T. S. (2017). Predicting a drug's membrane permeability: A computational model validated with in vitro permeability assay data. The Journal of Physical Chemistry B, 121(20), 5228–5237. https://doi.org/10.1021/acs.jpcb.7b02914
   PubMed Web of Science ®Google Scholar
• Beretta, G. L., Perego, P., & Zunino, F. (2008). Targeting topoisomerase I: Molecular mechanisms and cellular determinants of response to topoisomerase I inhibitors. Expert Opinion on Therapeutic Targets, 12(10), 1243–1256. https://doi.org/10.1517/14728222.12.10.1243
   PubMed Web of Science ®Google Scholar
• Bernheim, J. L., & Kenis, Y. (1974). Chemotherapy of melanoma | LA CHIMIOTHERAPIE DU MELANOME. Acta Chirurgica Belgica, (2), 73.
   Web of Science ®Google Scholar
• Büyükkapu Bay, S., Kebudi, R., Görgün, O., Zülfikar, B., Darendeliler, E., & Çakır, F. B. (2019). Vincristine, irinotecan, and temozolomide treatment for refractory/relapsed pediatric solid tumors: A single center experience. Journal of Oncology Pharmacy Practice: Official Publication of the International Society of Oncology Pharmacy Practitioners, 25(6), 1343–1348.
   PubMed Web of Science ®Google Scholar
• Carrassa, L., & Damia, G. (2011). Unleashing Chk1 in cancer therapy. Cell Cycle (Georgetown, Tex.), 10(13), 2121–2128.
   PubMed Web of Science ®Google Scholar
• Castedo, M., Perfettini, J.-L., Roumier, T., Andreau, K., Medema, R., & Kroemer, G. (2004). Cell death by mitotic catastrophe: A molecular definition. Oncogene, 23(16), 2825–2837.
   PubMed Web of Science ®Google Scholar
• Castro, A. L. G., Cruz, J. N., Sodré, D. F., Correa-Barbosa, J., Azonsivo, R., de Oliveira, M. S., de Sousa Siqueira, J. E., da Rocha Galucio, N. C., de Oliveira Bahia, M., Burbano, R. M. R., do Rosário Marinho, A. M., Percário, S., Dolabela, M. F., & Vale, V. V. (2021). Evaluation of the genotoxicity and mutagenicity of isoeleutherin and eleutherin isolated from Eleutherine plicata herb using bioassays and in silico approaches. Arabian Journal of Chemistry, 14(4), 103084. https://doi.org/10.1016/j.arabjc.2021.103084
   Web of Science ®Google Scholar
• Chilà, R., Celenza, C., Lupi, M., Damia, G., & Carrassa, L. (2013). Chk1-Mad2 interaction: A crosslink between the DNA damage checkpoint and the mitotic spindle checkpoint. Cell Cycle (Georgetown, Tex.), 12(7), 1083–1090.
   PubMed Web of Science ®Google Scholar
• Chrencik, J. E., Staker, B. L., Burgin, A. B., Pourquier, P., Pommier, Y., Stewart, L., & Redinbo, M. R. (2004). Mechanisms of camptothecin resistance by human topoisomerase I mutations. Journal of Molecular Biology, 339(4), 773–784.
   PubMed Web of Science ®Google Scholar
• Collura, A., Blaisonneau, J., Baldacci, G., & Francesconi, S. (2005). The fission yeast Crb2/Chk1 pathway coordinates the DNA damage and spindle checkpoint in response to replication stress induced by topoisomerase I inhibitor. Molecular and Cellular Biology, 25(17), 7889–7899.
   PubMed Web of Science ®Google Scholar
• Costa, E. B., Silva, R. C., Espejo-Román, J. M., Neto, M. D. A., Cruz, J. N., Leite, F. H. A., Silva, C. H. T. P., Pinheiro, J. C., Macêdo, W. J. C., & Santos, C. B. R. (2020). Chemometric methods in antimalarial drug design from 1,2,4,5-tetraoxanes analogues. SAR and QSAR in Environmental Research, 31(9), 677–695. https://doi.org/10.1080/1062936X.2020.1803961
   PubMed Web of Science ®Google Scholar
• Coulup, S. K., & Georg, G. I. (2019). Revisiting microtubule targeting agents: α-Tubulin and the pironetin binding site as unexplored targets for cancer therapeutics. Bioorganic & Medicinal Chemistry Letters, 29(15), 1865–1873. https://doi.org/10.1016/j.bmcl.2019.05.042
   PubMed Web of Science ®Google Scholar
• Csermely, P., Korcsmáros, T., Kiss, H. J. M., London, G., & Nussinov, R. (2013). Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review. Pharmacology & Therapeutics, 138(3), 333–408. https://doi.org/10.1016/j.pharmthera.2013.01.016
   PubMed Web of Science ®Google Scholar
• Da Silva Júnior, O. S., Franco, C. D. J. P., de Moraes, A. A. B., Cruz, J. N., da Costa, K. S., do Nascimento, L. D., & de Aguiar Andrade, E. H. (2021). In silico analyses of toxicity of the major constituents of essential oils from two Ipomoea L. species. Toxicon: Official Journal of the International Society on Toxinology, 195, 111–118. https://doi.org/10.1016/j.toxicon.2021.02.015
   PubMed Web of Science ®Google Scholar
• De Oliveira, M., da Cruz, J. N., da Costa, W., Silva, S. G., Brito, M. D. P., de Menezes, S. A. F., de Jesus Chaves Neto, A. M., de Aguiar Andrade, E. H., & de Carvalho Junior, R. N. (2020). Chemical composition, antimicrobial properties of Siparuna guianensis essential oil and a molecular docking and dynamics molecular study of its major chemical constituent. Molecules, 25(17), 3852. https://doi.org/10.3390/molecules25173852
   PubMed Web of Science ®Google Scholar
• Dilshara, M. G., Jayasooriya, R. G. P. T., Karunarathne, W. A. H. M., Choi, Y. H., & Kim, G. Y. (2019). Camptothecin induces mitotic arrest through Mad2-Cdc20 complex by activating the JNK-mediated Sp1 pathway. Food and Chemical Toxicology: An International Journal Published for the British Industrial Biological Research Association, 127, 143–155. https://doi.org/10.1016/j.fct.2019.03.026
   PubMed Web of Science ®Google Scholar
• Duan, Y. T., Man, R. J., Tang, D. J., Yao, Y. F., Tao, X. X., Yu, C., Liang, X. Y., Makawana, J. A., Zou, M. J., Wang, Z. C., & Zhu, H. L. (2016). Design, synthesis and antitumor activity of novel link-bridge and B-ring modified combretastatin A-4 (CA-4) analogues as potent antitubulin agents. Scientific Reports, 6, 25387–25313. https://doi.org/10.1038/srep25387
   PubMed Web of Science ®Google Scholar
• Engin, H., Gursoy, A., Nussinov, R., & Keskin, O. (2014). Network-based strategies can help mono- and poly-pharmacology drug discovery: A systems biology view. Current Pharmaceutical Design, 20(8), 1201–1207. https://doi.org/10.2174/13816128113199990066
   PubMed Web of Science ®Google Scholar
• Espinoza-Fonseca, L. M. (2006). The benefits of the multi-target approach in drug design and discovery. Bioorganic & Medicinal Chemistry, 14(4), 896–897. https://doi.org/10.1016/j.bmc.2005.09.011
   PubMed Web of Science ®Google Scholar
• Fendt, S.-M. (2019). Metabolic vulnerabilities of metastasizing cancer cells. BMC Biology, 17(1), 1–4. https://doi.org/10.1186/s12915-019-0672-2
   PubMedGoogle Scholar
• Florea, A.-M., & Büsselberg, D. (2011). Cisplatin as an anti-tumor drug: Cellular mechanisms of activity, drug resistance and induced side effects. Cancers, 3(1), 1351–1371. https://doi.org/10.3390/cancers3011351
   PubMedGoogle Scholar
• Fraczkiewicz, R., & Braun, W. (1998). Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. Journal of Computational Chemistry, 19(3), 319–333. http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1096-987X(199802)19:3%3C319::AID-JCC6%3E3.0.CO%5Cn2-W/abstract%5Cnpapers2://publication/uuid/5F874541-F97F-4E6C-AA85-D3D93FC3BDB9
   Web of Science ®Google Scholar
• da Silva Hage-Melim, L. I., Federico, L. B., de Oliveira, N. K. S., Francisco, V. C. C., Correia, L. C., de Lima, H. B., Gomes, S. Q., Barcelos, M. P., Francischini, I. A. G., & da Silva, C. H. T. d P. (2020). Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19. Life Sciences, 256, 117963. https://doi.org/10.1016/j.lfs.2020.117963
   PubMed Web of Science ®Google Scholar
• Hecht, J. R., Blanke, C. D., Benson, 3rd, A. B., & Lenz, H. J. (2003). Irinotecan and paclitaxel in metastatic adenocarcinoma of the esophagus and gastric cardia. Oncology (Williston Park, N.Y.), 17(9 Suppl 8), 13–15.
   PubMedGoogle Scholar
• Holla, H., Sharma, A., Bhat, P., Shinde, D., & Das, B. (2017). Two new substituted polychiral 5, 6-dihydro-α-pyrones from Orthosiphon diffusus and molecular docking studies. Phytochemistry Letters, 22(May), 21–26. https://doi.org/10.1016/j.phytol.2017.08.006
   Google Scholar
• Holla, H., Srinivas, Y., Majhi, A., Srinivasulu, G., Sridhar, B., Sai, A., Venkateswara, J., & Das, B. (2011). Novel cytotoxic constituents of Orthosiphon diffusus q. Tetrahedron Letters, 52(1), 49–52. https://doi.org/10.1016/j.tetlet.2010.10.140
   Web of Science ®Google Scholar
• Jordan, M. A., & Wilson, L. (2004). Microtubules as a target for anticancer drugs. Nature Reviews. Cancer, 4(4), 253–265. https://doi.org/10.1038/nr1317
   PubMed Web of Science ®Google Scholar
• Kobayashi, S., Tsuchiya, K., Kurokawa, T., Nakagawa, T., Shimada, N., & Iitaka, Y. (1994). Pironetin, a novel plant growth regulator produced by streptomyces sp. Nk10958. II. Structural elucidation. The Journal of Antibiotics, 47(6), 703–707. https://doi.org/10.7164/antibiotics.47.703
   PubMed Web of Science ®Google Scholar
• Kousholt, A. N., Menzel, T., & Sørensen, C. S. (2012). Pathways for genome integrity in G2 phase of the cell cycle. Biomolecules, 2(4), 579–607. https://doi.org/10.3390/biom2040579
   PubMedGoogle Scholar
• Leão, R. P., Cruz, J. V., da Costa, G. V., Cruz, J. N., Ferreira, E. F. B., Silva, R. C., de Lima, L. R., Borges, R. S., dos Santos, G. B., & Santos, C. B. R. (2020). Identification of new rofecoxib-based cyclooxygenase-2 inhibitors: A bioinformatics approach. Pharmaceuticals, 13(9), 209. https://doi.org/10.3390/ph13090209
   Web of Science ®Google Scholar
• 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. https://doi.org/10.1016/S0169-409X(00)00129-0
   PubMed Web of Science ®Google Scholar
• Lu, J. J., Pan, W., Hu, Y. J., & Wang, Y. T. (2012). Multi-target drugs: The trend of drug research and development. PLoS One, 7(6), e40262. https://doi.org/10.1371/journal.pone.0040262
   PubMed Web of Science ®Google Scholar
• Mita, M. M., Spear, M. A., Yee, L. K., Mita, A. C., Heath, E. I., Papadopoulos, K. P., Federico, K. C., Reich, S. D., Romero, O., Malburg, L., Pilat, M., Lloyd, G. K., Neuteboom, S. T. C., Cropp, G., Ashton, E., & LoRusso, P. M. (2010). Phase 1 first-in-human trial of the vascular disrupting agent plinabulin(NPI-2358) in patients with solid tumors or lymphomas. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 16(23), 5892–5899. https://doi.org/10.1158/1078-0432.CCR-10-1096
   PubMed Web of Science ®Google Scholar
• Norinder, U., & Haeberlein, M. (2002). Computational approaches to the prediction of the blood-brain distribution. Advanced Drug Delivery Reviews, 54(3), 291–313. https://doi.org/10.1016/S0169-409X(02)00005-4
   PubMed Web of Science ®Google Scholar
• Ntie-Kang, F. (2013). An in silico evaluation of the ADMET profile of the StreptomeDB database. SpringerPlus, 2(1), 353. https://doi.org/10.1186/2193-1801-2-353
   PubMedGoogle Scholar
• Osmundson, E. C., Ray, D., Moore, F. E., Gao, Q., Thomsen, G. H., & Kiyokawa, H. (2008). The HECT E3 ligase Smurf2 is required for Mad2-dependent spindle assembly checkpoint. The Journal of cell biology, 183(2), 267–277. https://doi.org/10.1083/jcb.200801049
   PubMed Web of Science ®Google Scholar
• Raciborska, A., Bilska, K., Drabko, K., Chaber, R., Pogorzala, M., Wyrobek, E., Polczyńska, K., Rogowska, E., Rodriguez-Galindo, C., & Wozniak, W. (2013). Vincristine, irinotecan, and temozolomide in patients with relapsed and refractory Ewing sarcoma. Pediatric Blood & Cancer, 60(10), 1621–1625.
   PubMed Web of Science ®Google Scholar
• Santana de Oliveira, M., Pereira da Silva, V. M., Cantão Freitas, L., Gomes Silva, S., Nevez Cruz, J., & de Aguiar Andrade, E. H. (2021). Extraction yield, chemical composition, preliminary toxicity of Bignonia nocturna (Bignoniaceae) essential oil and in silico evaluation of the interaction. Chemistry and Biodiversity, 18(4), e2000982. https://doi.org/10.1002/cbdv.202000982
   Google Scholar
• Santos, C. B. R., Santos, K. L. B., Cruz, J. N., Leite, F. H. A., Borges, R. S., Taft, C. A., Campos, J. M., & Silva, C. H. T. P. (2021). Molecular modeling approaches of selective adenosine receptor type 2A agonists as potential anti-inflammatory drugs. Journal of Biomolecular Structure & Dynamics, 39(9), 3115–3127. https://doi.org/10.1080/07391102.2020.1761878
   PubMed Web of Science ®Google Scholar
• Saxena, P., Hortigon-Vinagre, M. P., Beyl, S., Baburin, I., Andranovits, S., Iqbal, S. M., Costa, A., IJzerman, A. P., Kügler, P., Timin, E., Smith, G. L., & Hering, S. (2017). Correlation between human ether-a-go-go-related gene channel inhibition and action potential prolongation. British Journal of Pharmacology, 174(18), 3081–3093. https://doi.org/10.1111/bph.13942
   PubMed Web of Science ®Google Scholar
• Schrödinger Software Release 2015-2. (2015). QikProp 4.4 user manual (pp. 1–45). Schrodinger Press. http://gohom.win/ManualHom/Schrodinger/Schrodinger_2015-2_docs/qikprop/qikprop_user_manual.pdf
   Google Scholar
• Setty, B. A., Stanek, J. R., Mascarenhas, L., Miller, A., Bagatell, R., Okcu, F., Nicholls, L., Lysecki, D., & Gupta, A. A. (2018). VIncristine, irinotecan, and temozolomide in children and adolescents with relapsed rhabdomyosarcoma. Pediatric Blood & Cancer, 65(1), e26728. https://doi.org/10.1002/pbc.26728
   Web of Science ®Google Scholar
• Shiloh, Y. (2003). ATM and related protein kinases: Safeguarding genome integrity. Nature Reviews. Cancer, 3(3), 155–168. https://doi.org/10.1038/nrc1011
   PubMed Web of Science ®Google Scholar
• Speck-Planche, A., Kleandrova, V. V., Luan, F., & Cordeiro, M. N. D. S. (2011). Multi-target drug discovery in anti-cancer therapy: Fragment-based approach toward the design of potent and versatile anti-prostate cancer agents. Bioorganic & Medicinal Chemistry, 19(21), 6239–6244. https://doi.org/10.1016/j.bmc.2011.09.015
   PubMed Web of Science ®Google Scholar
• Sym, S. J., Chang, H. M., Kang, H. J., Lee, S. S., Ryu, M.-H., Lee, J.-L., Kim, T.-W., Yook, J. H., Oh, S. T., Kim, B. S., & Kang, Y.-K. (2008). A phase II study of irinotecan and docetaxel combination chemotherapy for patients with previously treated metastatic or recurrent advanced gastric cancer. Cancer Chemotherapy and Pharmacology, 63(1), 1–8. https://doi.org/10.1007/s00280-008-0701-2
   PubMed Web of Science ®Google Scholar
• Wang, Y., Naismith, J., & Zhu, X. (n. d.). (2015) A new complex structure of tubulin with an alpha-beta unsaturated lactone. Protein Data Bank. https://doi.org/10.2210/pdb5FNV/pdb
   Google Scholar
• Wang, X., Tanaka, M., Krstin, S., Peixoto, H. S., de Melo Moura, C. C., & Wink, M. (2016). Cytoskeletal interference–A new mode of action for the anticancer drugs camptothecin and topotecan. European Journal of Pharmacology, 789, 265–274.
   PubMed Web of Science ®Google Scholar
• Wink, M. (2007). Molecular modes of action of cytotoxic alkaloids: From DNA intercalation, spindle poisoning, topoisomerase inhibition to apoptosis and multiple drug resistance. The Alkaloids. Chemistry and Biology, 64, 1–47.
   PubMedGoogle Scholar
• Wright, J. C., & Madden, R. E. (1974). Cancer chemotherapy in man. Review of Surgery, 31(4), 217–237.
   PubMedGoogle Scholar
• Yang, J., Wang, Y., Wang, T., Jiang, J., Botting, C. H., Liu, H., Chen, Q., Yang, J., Naismith, J. H., & Zhu, X. (2016). Pironetin reacts covalently with cysteine-316 of α-tubulin to destabilize microtubule. Nature Communications, 7(1), 1–9.
   Google Scholar
• Yang, X., Xu, W., Hu, Z., Zhang, Y., & Xu, N. (2014). Chk1 is required for the metaphase–anaphase transition via regulating the expression and localization of Cdc20 and Mad2. Life Sciences, 106(1-2), 12–18.
   PubMed Web of Science ®Google Scholar