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Research Articles

Molecular docking and pharmacophore models to probe binding hypothesis of inhibitors of hypoxia inducible factor-1

, , , &
Pages 7714-7725 | Received 08 Dec 2020, Accepted 04 Mar 2021, Published online: 24 Apr 2021

References

  • Abraham, M. H., & Le, J. (1999). The correlation and prediction of the solubility of compounds in water using an amended solvation energy relationship. Journal of Pharmaceutical Sciences, 88(9), 868–880. https://doi.org/10.1021/js9901007
  • Accelrys Draw 4.1. (2011). http://accelrys.com/products/informatics/cheminformatics/draw/.
  • Altman, D. G., & Bland, J. M. (1994). Diagnostic tests. 1: Sensitivity and specificity. BMJ (Clinical Research Ed.), 308(6943), 1552. https://doi.org/10.1136/bmj.308.6943.1552
  • Ao, Q., Su, W., Guo, S., Cai, L., & Huang, L. (2015). SENP1 desensitizes hypoxic ovarian cancer cells to cisplatin by up-regulating HIF-1α. Scientific Reports, 5, 16396. https://doi.org/10.1038/srep16396
  • Augeri, D. J., Robl, J. A., Betebenner, D. A., Magnin, D. R., Khanna, A., Robertson, J. G., Wang, A., Simpkins, L. M., Taunk, P., Huang, Q., Han, S.-P., Abboa-Offei, B., Cap, M., Xin, L., Tao, L., Tozzo, E., Welzel, G. E., Egan, D. M., Marcinkeviciene, J., … Hamann, L. G. (2005). Discovery and preclinical profile of Saxagliptin (BMS-477118): a highly potent, long-acting, orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes. Journal of Medicinal Chemistry, 48(15), 5025–5037. https://doi.org/10.1021/jm050261p
  • Benita, Y., Kikuchi, H., Smith, A. D., Zhang, M. Q., Chung, D. C., & Xavier, R. J. (2009). An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Research, 37(14), 4587–4602. https://doi.org/10.1093/nar/gkp425
  • Bhattarai, D., Xu, X., & Lee, K. (2018). Hypoxia-inducible factor-1 (HIF-1) inhibitors from the last decade (2007 to 2016): A “structure-activity relationship” perspective. Medicinal Research Reviews, 38(4), 1404–1442. https://doi.org/10.1002/med.21477
  • Cardoso, R., Love, R., Nilsson, C. L., Bergqvist, S., Nowlin, D., Yan, J., Liu, K. K.-C., Zhu, J., Chen, P., Deng, Y.-L., Dyson, H. J., Greig, M. J., & Brooun, A. (2012). Identification of Cys255 in HIF-1α as a novel site for development of covalent inhibitors of HIF-1α/ARNT PasB domain protein-protein interaction . Protein Science: A Publication of the Protein Society, 21(12), 1885–1896. https://doi.org/10.1002/pro.2172
  • Chau, N.-M., Rogers, P., Aherne, W., Carroll, V., Collins, I., McDonald, E., Workman, P., & Ashcroft, M. (2005). Identification of novel small molecule inhibitors of hypoxia-inducible factor-1 that differentially block hypoxia-inducible factor-1 activity and hypoxia-inducible factor-1alpha induction in response to hypoxic stress and growth factors. Cancer Research, 65(11), 4918–4928. https://doi.org/10.1158/0008-5472.CAN-04-4453
  • Chen, I. J., & Foloppe, N. (2008). Conformational sampling of druglike molecules with MOE and catalyst: Implications for pharmacophore modeling and virtual screening. Journal of Chemical Information and Modeling, 48(9), 1773–1791. https://doi.org/10.1021/ci800130k
  • Chung, J. Y., Pasha, F. A., Cho, S. J., Won, M., Lee, J. J., & Lee, K. (2009). Pharmacophore-based 3D-QSAR of HIF-1 inhibitors. Archives of Pharmacal Research, 32(3), 317–323. https://doi.org/10.1007/s12272-009-1301-3
  • Corbeil, C. R., Williams, C. I., & Labute, P. (2012). Variability in docking success rates due to dataset preparation. Journal of Computer-Aided Molecular Design, 26(6), 775–786. https://doi.org/10.1007/s10822-012-9570-1
  • Ebert, B. L., & Bunn, H. F. (1998). Regulation of transcription by hypoxia requires a multiprotein complex that includes hypoxia-inducible factor 1, an adjacent transcription factor, and p300/CREB binding protein. Molecular and Cellular Biology, 18(7), 4089–4096. https://doi.org/10.1128/mcb.18.7.4089
  • Feher, M. (2006). Consensus scoring for protein-ligand interactions. Drug Discovery Today, 11(9–10), 421–428. https://doi.org/10.1016/j.drudis.2006.03.009
  • Ferguson, D. M., Marsh, A., Metzger, T., Garrett, D. G., & Kastella, K. (1994). Conformational searches for the global minimum of protein models. Journal of Global Optimization, 4(2), 209–227. https://doi.org/10.1007/BF01096723
  • Halgren, T. (1999). MMFF VII. characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries. Journal of Computational Chemistry, 20(7), 730–748. https://doi.org/10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T
  • Havale, S. H., and., & Pal, M. (2009). Medicinal chemistry approaches to the inhibition of dipeptidyl peptidase-4 for the treatment of type 2 diabetes. Bioorganic & Medicinal Chemistry, 17(5), 1783–1802. https://doi.org/10.1016/j.bmc.2009.01.061
  • Hubbi, M. E. (2013). A nontranscriptional role for HIF-1alpha as a direct inhibitor of DNA replication. Sci Signal, 6(262), ra10. https://doi.org/10.1126/scisignal.2003417
  • Ke, Q., & Costa, M. (2006). Hypoxia-inducible factor-1 (HIF-1). Molecular Pharmacology, 70(5), 1469–1480. https://doi.org/10.1124/mol.106.027029
  • Kung, A. L., Zabludoff, S. D., France, D. S., Freedman, S. J., Tanner, E. A., Vieira, A., Cornell-Kennon, S., Lee, J., Wang, B., Wang, J., Memmert, K., Naegeli, H.-U., Petersen, F., Eck, M. J., Bair, K. W., Wood, A. W., & Livingston, D. M. (2004). Small molecule blockade of transcriptional coactivation of the hypoxia-inducible factor pathway. Cancer Cell, 6(1), 33–43. https://doi.org/10.1016/j.ccr.2004.06.009
  • Labute, P. (2008). The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area. Journal of Computational Chemistry, 29(10), 1693–1698. https://doi.org/10.1002/jcc.20933
  • Lee, K. A., Zhang, H., Qian, D. Z., Rey, S., Liu, J. O., & Semenza, G. L. (2009). Acriflavine inhibits HIF-1 dimerization, tumor growth, and vascularization. Proceedings of the National Academy of Sciences of the United States of America, 106(42), 17910–17915. https://doi.org/10.1073/pnas.0909353106
  • Lipinski, C. A. (2004). Lead- and drug-like compounds: The rule-of-five revolution. Drug Discovery Today. Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
  • 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
  • Liu, J., Obando, D., Liao, V., Lifa, T., & Codd, R. (2011). The many faces of the adamantyl group in drug design. European Journal of Medicinal Chemistry, 46(6), 1949–1963. https://doi.org/10.1016/j.ejmech.2011.01.047
  • Loboda, A., Jozkowicz, A., & Dulak, J. (2010). HIF-1 and HIF-2 transcription factors-similar but not identical. Molecules and Cells, 29(5), 435–442. https://doi.org/10.1007/s10059-010-0067-2
  • Malo, M., Brive, L., Luthman, K., & Svensson, P. (2010). Selective pharmacophore models of dopamine D(1) and D(2) full agonists based on extended pharmacophore features. ChemMedChem, 5(2), 232–246. https://doi.org/10.1002/cmdc.200900398
  • Mansour, R., Enderami, S., Ardeshirylajimi, A., Fooladsaz, K., Fathi, M., & Ganji, S. (2016). Evaluation of hypoxia inducible factor-1 alpha gene expression in colorectal cancer stages of Iranian patients. Journal of Cancer Research and Therapeutics, 12(4), 1313–1317. https://doi.org/10.4103/0973-1482.199542
  • Masoud, G. N., & Li, W. (2015). HIF-1α pathway: Role, regulation and intervention for cancer therapy. Acta Pharmaceutica Sinica B, 5(5), 378–389. https://doi.org/10.1016/j.apsb.2015.05.007
  • Matthews, B. W. (1975). Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochimica et Biophysica Acta, 405(2), 442–451. https://doi.org/10.1016/0005-2795(75)90109-9
  • Metz, C. E. (1978). Basic principles of ROC analysis. Seminars in Nuclear Medicine, 8(4), 283–298. https://doi.org/10.1016/S0001-2998(78)80014-2
  • Miranda, E., Nordgren, I. K., Male, A. L., Lawrence, C. E., Hoakwie, F., Cuda, F., Court, W., Fox, K. R., Townsend, P. A., Packham, G. K., Eccles, S. A., & Tavassoli, A. (2013). A cyclic peptide inhibitor of HIF-1 heterodimerization that inhibits hypoxia signaling in cancer cells. Journal of the American Chemical Society, 135(28), 10418–10425. https://doi.org/10.1021/ja402993u
  • Mistry, I. N., & Tavassoli, A. (2017). Reprogramming the transcriptional response to hypoxia with a chromosomally encoded cyclic peptide HIF-1 inhibitor. ACS Synthetic Biology, 6(3), 518–527. https://doi.org/10.1021/acssynbio.6b00219
  • Molecular Operating Environment (MOE). (2020). 2019.01. Chemical Computing Group ULC.
  • Mooring, S. R., Jin, H., Devi, N. S., Jabbar, A. A., Kaluz, S., Liu, Y., Van Meir, E. G., & Wang, B. (2011). Design and synthesis of novel small-molecule inhibitors of the hypoxia inducible factor pathway. Journal of Medicinal Chemistry, 54(24), 8471–8489. https://doi.org/10.1021/jm201018g
  • Mosmann, T. (1983). Rapid colorimetric assay for cellular growth and survival: Application to proliferation and cytotoxicity assays. Journal of Immunological Methods, 65(1–2), 55–63. https://doi.org/10.1016/0022-1759(83)90303-4
  • Munawar, S., Windley, M. J., Tse, E. G., Todd, M. H., Hill, A. P., Vandenberg, J. I., & Jabeen, I. (2018). Experimentally validated pharmacoinformatics approach to predict hERG inhibition potential of new chemical entities. Frontiers in Pharmacology, 9, 1035. https://doi.org/10.3389/fphar.2018.01035
  • Munoz-Sanchez, J., & Chanez-Cardenas, M. E. (2019). The use of cobalt chloride as a chemical hypoxia model. Journal of Applied Toxicology, 39(4), 556–570.
  • Pierard, G. E. (2009). Spotlight on adapalene. Expert Opinion on Drug Metabolism & Toxicology, 5(12), 1565–1575.
  • Piret, J.-P., Mottet, D., Raes, M., & Michiels, C. (2002). CoCl2, a chemical inducer of hypoxia-inducible factor-1, and hypoxia reduce apoptotic cell death in hepatoma cell line HepG2. Annals of the New York Academy of Sciences, 973, 443–447. https://doi.org/10.1111/j.1749-6632.2002.tb04680.x
  • Rapisarda, A., Zalek, J., Hollingshead, M., Braunschweig, T., Uranchimeg, B., Bonomi, C. A., Borgel, S. D., Carter, J. P., Hewitt, S. M., Shoemaker, R. H., & Melillo, G. (2004). Schedule-dependent inhibition of hypoxia-inducible factor-1alpha protein accumulation, angiogenesis, and tumor growth by topotecan in U251-HRE glioblastoma xenografts. Cancer Research, 64(19), 6845–6848. https://doi.org/10.1158/0008-5472.CAN-04-2116
  • Rosenthal, K. S., Sokol, M. S., Ingram, R. L., Subramanian, R., & Fort, R. C. (1982). Tromantadine: Inhibitor of early and late events in herpes simplex virus replication. Antimicrobial Agents and Chemotherapy, 22(6), 1031–1036. https://doi.org/10.1128/aac.22.6.1031
  • Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F., & Schroeder, M. (2015). PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Research, 43(W1), W443–W447. https://doi.org/10.1093/nar/gkv315
  • Schneider, G. (2000–2013). Prediction of drug-like properties. Landes Bioscience.
  • Semenza, G. L. (2012). Hypoxia-inducible factors in physiology and medicine. Cell, 148(3), 399–408. https://doi.org/10.1016/j.cell.2012.01.021
  • Shi, Q., Yin, S., Kaluz, S., Ni, N., Devi, N. S., Mun, J., Wang, D., Damera, K., Chen, W., Burroughs, S., Mooring, S. R., Goodman, M. M., Van Meir, E. G., Wang, B., & Snyder, J. P. (2012). Binding model for the interaction of anticancer arylsulfonamides with the p300 transcription cofactor. ACS Medicinal Chemistry Letters, 3(8), 620–625. https://doi.org/10.1021/ml300042k
  • Sushko, I., Novotarskyi, S., Körner, R., Pandey, A. K., Rupp, M., Teetz, W., Brandmaier, S., Abdelaziz, A., Prokopenko, V. V., Tanchuk, V. Y., Todeschini, R., Varnek, A., Marcou, G., Ertl, P., Potemkin, V., Grishina, M., Gasteiger, J., Schwab, C., Baskin, I. I., … Tetko, I. V. (2011). Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. Journal of Computer-Aided Molecular Design, 25(6), 533–554. https://doi.org/10.1007/s10822-011-9440-2
  • Talks, K. L., Turley, H., Gatter, K. C., Maxwell, P. H., Pugh, C. W., Ratcliffe, P. J., & Harris, A. L. (2000). The expression and distribution of the hypoxia-inducible factors HIF-1alpha and HIF-2alpha in normal human tissues, cancers, and tumor-associated macrophages. The American Journal of Pathology, 157(2), 411–421. https://doi.org/10.1016/S0002-9440(10)64554-3
  • Tan, C., de Noronha, R. G., Devi, N. S., Jabbar, A. A., Kaluz, S., Liu, Y., Mooring, S. R., Nicolaou, K. C., Wang, B., & Van Meir, E. G. (2011). Sulfonamides as a new scaffold for hypoxia inducible factor pathway inhibitors. Bioorganic & Medicinal Chemistry Letters, 21(18), 5528–5532. https://doi.org/10.1016/j.bmcl.2011.06.099
  • Tang, W., & Zhao, G. (2020). Small molecules targeting HIF-1α pathway for cancer therapy in recent years. Bioorganic & Medicinal Chemistry, 28(2), 115235. https://doi.org/10.1016/j.bmc.2019.115235
  • Wang, D.-Y., Li, Y.-W., Zhang, L.-H., Lv, L.-Y., Zhao, Y.-Q., Jin, X.-J., & Piao, H.-R. (2020). Synthesis and evaluation of HIF-1α inhibitory activities of novel panaxadiol derivatives. Bioorganic & Medicinal Chemistry Letters, 30(24), 127652. https://doi.org/10.1016/j.bmcl.2020.127652
  • Wang, G. L., Jiang, B. H., Rue, E. A., & Semenza, G. L. (1995). Hypoxia-inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular O2 tension. Proceedings of the National Academy of Sciences of the United States of America, 92(12), 5510–5514. https://doi.org/10.1073/pnas.92.12.5510
  • Wang, S., Liu, L., Guo, X., Li, G., Wang, X., Dong, H., Li, Y., & Zhao, W. (2019). Synthesis of novel natural product-like diaryl acetylenes as hypoxia inducible factor-1 inhibitors and antiproliferative agents. RSC Advances, 9(24), 13878–13886. https://doi.org/10.1039/C9RA02525A
  • Wang, W., Ao, L., Rayburn, E. R., Xu, H., Zhang, X., Zhang, X., Nag, S. A., Wu, X., Wang, M.-H., Wang, H., Van Meir, E. G., & Zhang, R. (2012). KCN1, a novel synthetic sulfonamide anticancer agent: In vitro and in vivo anti-pancreatic cancer activities and preclinical pharmacology. PLoS One, 7(9), e44883. https://doi.org/10.1371/journal.pone.0044883
  • Welsh, S. (2004). Antitumor activity and pharmacodynamic properties of PX-478, an inhibitor of hypoxia-inducible factor-1alpha. Molecular Cancer Therapeutics, 3(3), 233–244.
  • Yang, G., Xu, S., Peng, L., Li, H., Zhao, Y., & Hu, Y. (2016). The hypoxia-mimetic agent CoCl2 induces chemotherapy resistance in LOVO colorectal cancer cells. Molecular Medicine Reports, 13(3), 2583–2589. https://doi.org/10.3892/mmr.2016.4836
  • Yin, S., Kaluz, S., Devi, N. S., Jabbar, A. A., de Noronha, R. G., Mun, J., Zhang, Z., Boreddy, P. R., Wang, W., Wang, Z., Abbruscato, T., Chen, Z., Olson, J. J., Zhang, R., Goodman, M. M., Nicolaou, K. C., & Van Meir, E. G. (2012). Arylsulfonamide KCN1 inhibits in vivo glioma growth and interferes with HIF signaling by disrupting HIF-1α interaction with cofactors p300/CBP. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 18(24), 6623–6633. https://doi.org/10.1158/1078-0432.CCR-12-0861
  • Zettl, H., Schubert-Zsilavecz, M., & Steinhilber, D. (2010). Medicinal chemistry of incretin mimetics and DPP-4 inhibitors. ChemMedChem, 5(2), 179–185. https://doi.org/10.1002/cmdc.200900448
  • Zhong, H., De Marzo, A. M., Laughner, E., Lim, M., Hilton, D. A., Zagzag, D., Buechler, P., Isaacs, W. B., Semenza, G. L., & Simons, J. W. (1999). Overexpression of hypoxia-inducible factor 1alpha in common human cancers and their metastases. Cancer Research, 59(22), 5830–5835.
  • Zoidis, G., Kolocouris, N., Kelly, J. M., Prathalingam, S. R., Naesens, L., & De Clercq, E. (2010). Design and synthesis of bioactive adamantanaminoalcohols and adamantanamines. European Journal of Medicinal Chemistry, 45(11), 5022–5030. https://doi.org/10.1016/j.ejmech.2010.08.009

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