199
Views
1
CrossRef citations to date
0
Altmetric
Research Articles

Molecular modeling studies of benzothiophene-containing derivatives as promising selective estrogen receptor downregulators: a combination of 3D-QSAR, molecular docking and molecular dynamics simulations

, , &
Pages 2702-2723 | Received 10 Jan 2020, Accepted 31 Mar 2020, Published online: 20 Apr 2020

References

  • Ashtekar, S. S., Bhatia, N. M., & Bhatia, M. S. (2018). Development of leads targeting ER-α in breast cancer: An in silico exploration from natural domain. Steroids, 131, 14–22. 10.1016/j.steroids.2017.12.016
  • Bentrem, D. J., Dardes, R. C., Liu, H., Macgregor-Schafer, J., Zapf, J. W., & Jordan, V. C. (2001). Molecular mechanism of action at estrogen receptor α of a new clinically relevant antiestrogen (GW7604) related to tamoxifen. Endocrinology, 142(2), 838–846. 10.1210/en.142.2.838
  • Bentzon, N., Düring, M., Rasmussen, B. B., Mouridsen, H., & Kroman, N. (2007). Prognostic effect of estrogen receptor status across age in primary breast cancer. International Journal of Cancer, 122(5), 1089–1094. 10.1002/ijc.22892
  • Bogliolo, S., Cassani, C., Dominoni, M., Orlandini, A., Ferrero, S., Iacobone, A. D., Viazzo, F., Venturini, P. L., Spinillo, A., & Gardella, B. (2017). The role of fulvestrant in endometrial cancer. Expert Opinion on Drug Metabolism & Toxicology, 13(5), 537–544. 10.1080/17425255.2016.1244264
  • Burks, H. E., Abrams, T., Kirby, C. A., Baird, J., Fekete, A., Hamann, L. G., Kim, S., Lombardo, F., Loo, A., Lubicka, D., Macchi, K., McDonnell, D. P., Mishina, Y., Norris, J. D., Nunez, J., Saran, C., Sun, Y., Thomsen, N. M., Wang, C., Wang, J., & Peukert, S. (2018). Discovery of an acrylic acid based tetrahydroisoquinoline as an orally bioavailable selective estrogen receptor degrader for ERα+ breast cancer. Journal of Medicinal Chemistry, 60(7), 2790–2818. 10.1021/acs.jmedchem.6b01468
  • Carlson, R. W. (2005). The history and mechanism of action of fulvestrant. Clinical Breast Cancer, 6, S5–S8. 10.3816/cbc.2005.s.008
  • Chai, T., & Draxler, R. R. (2014). Root mean square error (RMSE) or mean absolute error (MAE)? – Arguments against avoiding RMSE in the literature. Geoscientific Model Development, 7(3), 1247–1250. 10.5194/gmd-7-1247-2014
  • Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). admetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. Journal of Chemical Information and Modeling, 52(11), 3099–3105. 10.1021/ci300367a
  • Chinnasamy, S., Selvaraj, G., Kaushik, A. C., Kaliamurthi, S., Chandrabose, S., Singh, S. K., Thirugnanasambandam, R., Gu, K., & Wei, D.-Q. (2019). Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations. Journal of Biomolecular Structure and Dynamics, 38(1), 1–17. 10.1080/07391102.2019.1574605
  • Dai, Y.-H., Liao, L.-Z., & Li, D. (2004). On restart procedures for the conjugate gradient method. Numerical Algorithms, 35(2–4), 249–260. 10.1023/b:numa.0000021761.10993.6e
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 1–13. 10.1038/srep42717
  • Divakar, S., Santhoshkumar, M., Satvik, K., Ramachandra, S., Sasikumar, A., & Saravanan, J. (2020). Syringaresinol as a novel androgen receptor antagonist against wild and mutant androgen receptors for the treatment of castration resistant prostate cancer: Molecular docking, in-vitro and molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 739–1102. 10.1080/07391102.2020.1715261
  • Dutertre, M., & Smith, C. L. (2000). Molecular mechanisms of selective estrogen receptor modulator (SERM) action. The Journal of Pharmacology and Experimental Therapeutics, 295(2), 431–437. 10.0000/PMID11046073.
  • Fedele, P., Orlando, L., Schiavone, P., Calvani, N., Caliolo, C., Quaranta, A., Nacci, A., & Cinieri, S. (2015). Recent advances in the treatment of hormone receptor positive HER2 negative metastatic breast cancer. Critical Reviews in Oncology/Hematology, 94(3), 291–301. 10.1016/j.critrevonc.2015.01.001
  • Gasteiger, J., & Marsili, M. (1980). Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron, 36(22), 3219–3228. 10.1016/0040-4020(80)80168-2
  • Geetha Rani, Y., & Lakshmi, B. S. (2019). Structural insight into the antagonistic action of diarylheptanoid on human estrogen receptor alpha. Journal of Biomolecular Structure and Dynamics, 37(5), 1189–1115. 10.1080/07391102.2018.1453378
  • Golbraikh, A., Shen, M., Xiao, Z., Xiao, Y.-D., Lee, K.-H., & Tropsha, A. (2003). Rational selection of training and test sets for the development of validated QSAR models. Journal of Computer-Aided Molecular Design, 17(2/4), 241–253. 10.1023/A:1025386326946
  • Golbraikh, A., & Tropsha, A. (2002a). Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. Journal of Computer-Aided Molecular Design, 16(5/6), 357–369. [Mismatch] 10.1023/a:1020869118689
  • Golbraikh, A., & Tropsha, A. (2002b). Beware of q2! Journal of Molecular Graphics and Modelling, 20(4), 269–276. 10.1016/S1093-3263(01)00123-1
  • Halim, S. A. (2015). Structure based 3D-QSAR studies of Interleukin-2 inhibitors: Comparing the quality and predictivity of 3D-QSAR models obtained from different alignment methods and charge calculations. Chemico-Biological Interactions, 238, 9–24. 10.1016/j.cbi.2015.05.018
  • Hamilton, E. P., Patel, M. R., Armstrong, A. C., Baird, R. D., Jhaveri, K., Hoch, M., Klinowska, T., Lindemann, J. P. O., Morgan, S. R., Schiavon, G., Weir, H. M., & Im, S.-A. (2018). A first-in-human study of the new oral selective estrogen receptor degrader AZD9496 for ER+/HER2 − advanced breast cancer. Clinical Cancer Research, 24(15), 3510–3518. 10.1158/1078-0432.ccr-17-3102
  • Howell, A., & Sapunar, F. (2011). Fulvestrant revisited: Efficacy and safety of the 500-mg dose. Clinical Breast Cancer, 11(4), 204–210. 10.1016/j.clbc.2011.02.002
  • Jeselsohn, R., Buchwalter, G., De Angelis, C., Brown, M., & Schiff, R. (2015). ESR1 mutations—a mechanism for acquired endocrine resistance in breast cancer. Nature Reviews Clinical Oncology, 12(10), 573–583. 10.1038/nrclinonc.2015.117
  • Johnston, S. R. D., & Dowsett, M. (2003). Aromatase inhibitors for breast cancer: Lessons from the laboratory. Nature Reviews Cancer, 3(11), 821–831. 10.1038/nrc1211
  • Jordan, V. C. (2018). Tamoxifen resistance trumped and oral selective estrogen receptor degraders arrive. Clinical Cancer Research, 24(15), 3480–3482. 10.1158/1078-0432.ccr-18-0759
  • Lai, A., Kahraman, M., Govek, S., Nagasawa, J., Bonnefous, C., Julien, J., Douglas, K., Sensintaffar, J., Lu, N., Lee, K-j., Aparicio, A., Kaufman, J., Qian, J., Shao, G., Prudente, R., Moon, M. J., Joseph, J. D., Darimont, B., Brigham, D., … Smith, N. D. (2015). Identification of GDC-0810 (ARN-810), an orally bioavailable selective estrogen receptor degrader (SERD) that demonstrates robust activity in tamoxifen-resistant breast cancer xenografts. Journal of Medicinal Chemistry, 58(12), 4888–4904. 10.1021/acs.jmedchem.5b00054
  • Lee, S., & Barron, M. G. (2018). 3D-QSAR study of steroidal and azaheterocyclic human aromatase inhibitors using quantitative profile of protein–ligand interactions. Journal of Cheminformatics, 10(1), 1–13. 10.1186/s13321-017-0253-8
  • Di Leo, A., Jerusalem, G., Petruzelka, L., Torres, R., Bondarenko, I. N., Khasanov, R., Verhoeven, D., Pedrini, J. L., Smirnova, I., Lichinitser, M. R., Pendergrass, K., Garnett, S., Lindemann, J. P. O., Sapunar, F., & Martin, M. (2010). Results of the CONFIRM phase III trial comparing Fulvestrant 250 mg with Fulvestrant 500 mg in postmenopausal women with estrogen receptor–positive advanced breast cancer. Journal of Clinical Oncology, 28(30), 4594–4600. 10.1200/jco.2010.28.8415
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17. 10.1016/j.addr.2012.09.019
  • McDonnell, D. P., Wardell, S. E., & Norris, J. D. (2015). Oral selective estrogen receptor downregulators (SERDs), a breakthrough endocrine therapy for breast cancer. Journal of Medicinal Chemistry, 58(12), 4883–4887. 10.1021/acs.jmedchem.5b00760
  • Milica, R., Dusan, R., Mirjana, A., Teodora, D., & Katarina, N. (2020). In silico identification of Novel 5-HT2A antagonists supported with ligand- and target- based drug design methodologies. Journal of Biomolecular Structure and Dynamics, 1–24. 10.1080/07391102.2020.1738961
  • Mills, J. N., Rutkovsky, A. C., & Giordano, A. (2018). Mechanisms of resistance in estrogen receptor positive breast cancer: Overcoming resistance to tamoxifen/aromatase inhibitors. Current Opinion in Pharmacology, 41, 59–65. 10.1016/j.coph.2018.04.009
  • Orlando, L., Schiavone, P., Fedele, P., Calvani, N., Nacci, A., Rizzo, P., Marino, A., D'Amico, M., Sponziello, F., Mazzoni, E., Cinefra, M., Fazio, N., Maiello, E., Silvestris, N., Colucci, G., & Cinieri, S. (2010). Molecularly targeted endocrine therapies for breast cancer. Cancer Treatment Reviews, 36, S67–S71. 10.1016/s0305-7372(10)70023-2
  • Ojha, P. K., & Roy, K. (2011). Comparative QSARs for antimalarial endochins: Importance of descriptor-thinning and noise reduction prior to feature selection. Chemometrics and Intelligent Laboratory Systems, 109(2), 146–161. 10.1016/j.chemolab.2011.08.007
  • Patel, H. K., & Bihani, T. (2018). Selective estrogen receptor modulators (SERMs) and selective estrogen receptor degraders (SERDs) in cancer treatment. Pharmacology & Therapeutics, 186, 1–24. 10.1016/j.pharmthera.2017.12.012
  • Pratim Partha, R., & Roy, K. (2008). On some aspects of variable selection for partial least squares regression models. QSAR & Combinatorial Science, 27(3), 302–313. 10.1002/qsar.200710043
  • Ranjan, P., Athar, M., Jha, P. C., & Krishna, K. V. (2018). Probing the opportunities for designing anthelmintic leads by sub-structural topology-based QSAR modelling. Molecular Diversity, 22(3), 669–683. 10.1007/s11030-018-9825-4
  • Robertson, J. F. R., & Harrison, M. (2004). Fulvestrant: Pharmacokinetics and pharmacology. British Journal of Cancer, 90(S1), S7–S10. 10.1038/sj.bjc.6601630
  • Romero-Parra, J., Chung, H., Tapia, R. A., Faúndez, M., Morales-Verdejo, C., Lorca, M., Lagos, C. F., Di Marzo, V., David Pessoa-Mahana, C., & Mella, J. (2017). Combined CoMFA and CoMSIA 3D-QSAR study of benzimidazole and benzothiophene derivatives with selective affinity for the CB2 cannabinoid receptor. European Journal of Pharmaceutical Sciences, 101, 1–10. 10.1016/j.ejps.2017.01.037
  • Sharma, D., Kumar, S., & Narasimhan, B. (2018). Estrogen alpha receptor antagonists for the treatment of breast cancer: A review. Chemistry Central Journal, 12(1), 107. 10.1186/s13065-018-0472-8
  • Shayanfar, A., & Shayanfar, S. (2014). Is regression through origin useful in external validation of QSAR models? European Journal of Pharmaceutical Sciences, 59, 31–35. 10.1016/j.ejps.2014.03.007
  • Tria, G. S., Abrams, T., Baird, J., Burks, H. E., Firestone, B., Gaither, L. A., Hamann, L. G., He, G., Kirby, C. A., Kim, S., Lombardo, F., Macchi, K. J., McDonnell, D. P., Mishina, Y., Norris, J. D., Nunez, J., Springer, C., Sun, Y., Thomsen, N. M., … Peukert, S. (2018). Discovery of LSZ102, a potent, orally bioavailable selective estrogen receptor degrader (SERD) for the treatment of estrogen receptor positive breast cancer. Journal of Medicinal Chemistry, 61(7), 2837–2864. 10.1021/acs.jmedchem.7b01682
  • Tropsha, A. (2010). Best practices for QSAR model development, validation, and exploitation. Molecular Informatics, 29(6–7), 476–488. 10.1002/minf.201000061
  • Vinter, J. G., Davis, A., & Saunders, M. R. (1987). Strategic approaches to drug design. I. An integrated software framework for molecular modelling. Journal of Computer-Aided Molecular Design, 1(1), 31–51. 10.1007/bf01680556
  • Weir, H. M., Bradbury, R. H., Lawson, M., Rabow, A. A., Buttar, D., Callis, R. J., Curwen, J. O., de Almeida, C., Ballard, P., Hulse, M., Donald, C. S., Feron, L. J. L., Karoutchi, G., MacFaul, P., Moss, T., Norman, R. A., Pearson, S. E., Tonge, M., Davies, G., … De Savi, C. (2016). AZD9496: An oral estrogen receptor inhibitor that blocks the growth of ER-positive and ESR1-mutant breast tumors in preclinical models. Cancer Research, 76(11), 3307–3318. 10.1158/0008-5472.can-15-2357
  • Wold, S., Sjöström, M., & Eriksson, L. (2001). PLS-regression: A basic tool of chemometrics. Chemometrics and Intelligent Laboratory Systems, 58(2), 109–130. 10.1016/s0169-7439(01)00155-1
  • Xiong, R., Zhao, J., Gutgesell, L. M., Wang, Y., Lee, S., Karumudi, B., Zhao, H., Lu, Y., Tonetti, D. A., & Thatcher, G. R. J. (2017). Novel selective estrogen receptor downregulators (SERDs) developed against treatment-resistant breast cancer. Journal of Medicinal Chemistry, 60(4), 1325–1342. 10.1021/acs.jmedchem.6b01355
  • Yinli, G., Hanxun, W., Jian, W., & Maosheng, C. (2019). In silico studies on p21-activated kinase 4 inhibitors: Comprehensive application of 3D-QSAR analysis, molecular docking, molecular dynamics simulations and MM-GBSA calculation. Journal of Biomolecular Structure and Dynamics, 1–26. 10.1080/07391102.2019.1673823
  • Zheng, L. H., Zhao, Y. H., Feng, H. L., & Liu, Y. J. (2014). Endocrine resistance in breast cancer. Climacteric, 17(5), 522–528. 10.3109/13697137.2013.864268

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.