Identification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches

References

• Atia, A., Alrawaiq, N., & Azman, A. (2014). A review of NAD(P)H:quinone oxidoreductase 1 (NQO1); A multifunctional antioxidant enzyme. Journal of Applied Pharmaceutical Science, 501(1), 116–123. http://doi.org/10.7324/JAPS.2014.41220
   Google Scholar
• Arora, R., Issar, U., & Kakkar, R. (2018). Identification of novel urease inhibitors: Pharmacophore modeling, virtual screening and molecular docking studies. Journal of Biomolecular Structure and Dynamics, 24, 1–15. doi:10.1080/07391102.2018.1546620
   Google Scholar
• Asher, G. (2005). A mechanism of ubiquitin-independent proteasomal degradation of the tumor suppressors p53 and p73. Genes & Development, 19(3), 316–321. doi:10.1101/gad.319905
   PubMed Web of Science ®Google Scholar
• Bharate, S. B., Yadav, R. R., & Vishwakarma, R. A. (2013). QSAR and pharmacophore study of Dyrk1A inhibitory meridianin analogs as potential agents for treatment of neurodegenerative diseases. Medicinal Chemistry, 9(1), 152–161. doi:10.2174/157340613804488459
   PubMed Web of Science ®Google Scholar
• Bian, J., Qian, X., Deng, B., Xu, X., Guo, X., Wang, Y., … Zhang, X. (2015). Discovery of NAD(P)H:quinone oxidoreductase 1 (NQO1) inhibitors with novel chemical scaffolds by shape-based virtual screening combined with cascade docking. RSC Advances, 5(61), 49471–49479. doi:10.1039/C5RA05919D
   Web of Science ®Google Scholar
• Chaudhary, N., & Aparoy, P. (2016). Deciphering the mechanism behind the varied binding activities of COXIBs through molecular dynamic simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies. Journal of Biomolecular Structure and Dynamics, 35(4), 868–882. doi:10.1080/07391102.2016.1165736
   PubMed Web of Science ®Google Scholar
• Chen, H., Lum, A., Seifried, A., Wilkens, L. R., & Le Marchand, L. (1999). Association of the NAD(P)H:quinone oxidoreductase 609C->T polymorphism with a decreased lung cancer risk. Cancer Research, 59(13), 3045–3048.
   PubMed Web of Science ®Google Scholar
• Cho, C. G., Lee, S. K., Nam, S.-Y., Lee, M.-S., Lee, S.-W., Choi, E. K., … Kim, S. Y. (2006). Association of the GSTP1 and NQO1 polymorphisms and head and neck squamous cell carcinoma risk. Journal of Korean Medical Science, 21(6), 1075. doi:10.3346/jkms.2006.21.6.1075
   PubMed Web of Science ®Google Scholar
• Deng, W., & Verlinde, C. L. M. J. (2008). Evaluation of different virtual screening programs for docking in a charged binding pocket. Journal of Chemical Information and Modeling, 48(10), 2010–2020. doi:10.1021/ci800154w
   PubMed Web of Science ®Google Scholar
• Dixon, S. L., Smondyrev, A. M., Knoll, E. H., Rao, S. N., Shaw, D. E., & Friesner, R. A. (2006). PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design, 20(10–11), 647–671. doi:10.1007/s10822-006-9087-6
   PubMed Web of Science ®Google Scholar
• Dixon, S. L., Smondyrev, A. M., & Rao, S. N. (2006). PHASE: A novel approach to pharmacophore modeling and 3D database searching. Chemical Biology & Drug Design, 67(5), 370–372. doi:10.1111/j.1747-0285.2006.00384.x
   PubMed Web of Science ®Google Scholar
• Dong, G.-Z., Oh, E.-T., Lee, H., Park, M.-T., Song, C. W., & Park, H. J. (2010). β-Lapachone suppresses radiation-induced activation of nuclear factor-κB. Experimental and Molecular Medicine, 42(5), 327. doi:10.3858/emm.2010.42.5.034
   PubMed Web of Science ®Google Scholar
• Ernster, L. (1967). [56] DT diaphorase. Methods in Enzymology, 10, 309–317. http://doi.org/10.1016/0076-6879(67)10059-1
   Google Scholar
• Ernster, L., Navazio, F., Löw, H., Siekevitz, P., Ernster, L., & Diczfalusy, E. (1958). Soluble diaphorase in animal tissues. Acta Chemica Scandinavica, 12, 595–595. doi:10.3891/acta.chem.scand.12-0595
   Google Scholar
• Evans, D. A., Doman, T. N., Thorner, D. A., & Bodkin, M. J. (2007). 3D QSAR methods: Phase and catalyst compared. Journal of Chemical Information and Modeling, 47(3), 1248–1257. doi:10.1021/ci7000082
   PubMed Web of Science ®Google Scholar
• Fan, Y., Hu, D., Feng, B., & Wang, W. (2014). The NQO1 C609T polymorphism and hepatocellular carcinoma risk. Tumor Biology, 35(8), 7343–7350. doi:10.1007/s13277-014-1712-8
   PubMedGoogle Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., … Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. doi:10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., … Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein − ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. doi:10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Galeazzi, R. (2009). Molecular dynamics as a tool in rational drug design: Current status and some major applications. Current Computer Aided-Drug Design, 5(4), 225–240. doi:10.2174/157340909789577847
   Web of Science ®Google Scholar
• Gupta, C. L., Babu Khan, M., Ampasala, D. R., Akhtar, S., Dwivedi, U. N., & Bajpai, P. (2019). Pharmacophore-based virtual screening approach for identification of potent natural modulatory compounds of human Toll-like receptor 7. Journal of Biomolecular Structure and Dynamics, 21, 1–16. doi:10.1080/07391102.2018.1559098
   Google Scholar
• Hamajima, N., Matsuo, K., Iwata, H., Shinoda, M., Yamamura, Y., Kato, T., … Tajima, K. (2002). NAD(P)H: Quinone oxidoreductase 1 (NQO1) C609T polymorphism and the risk of eight cancers for Japanese. International Journal of Clinical Oncology, 7(2), 103–108. http://doi.org/10.1007/s101470200013
   PubMedGoogle Scholar
• Hu, Y., Zhou, L., Zhu, X., Dai, D., Bao, Y., & Qiu, Y. (2018). Pharmacophore modeling, multiple docking and molecular dynamics studies on Wee1 kinase inhibitors. Journal of Biomolecular Structure and Dynamics, 27, 1–25. doi:10.1080/07391102.2018.1495576
   Google Scholar
• Iqbal, S., Anantha Krishnan, D., & Gunasekaran, K. (2018). Identification of potential PKC inhibitors through pharmacophore designing, 3D-QSAR and molecular dynamics simulations targeting Alzheimer’s disease. Journal of Biomolecular Structure and Dynamics, 36(15), 4029–4044. doi:10.1080/07391102.2017.1406824
   PubMed Web of Science ®Google Scholar
• Jaiswal, A. K. (1991). Human NAD(P)H:quinone oxidoreductase (NQO1) gene structure and induction by dioxin. Biochemistry, 30(44), 10647–10653. doi:10.1021/bi00108a007
   PubMed Web of Science ®Google Scholar
• Kohar, I., Baca, M., Suarna, C., Stocker, R., & Southwell-Keely, P. T. (1995). Is α-tocopherol a reservoir for α-tocopheryl hydroquinone? Free Radical Biology and Medicine, 19(2), 197–207. http://doi.org/10.1016/0891-5849(95)00010-U doi:10.1016/0891-5849(95)00010-U
   PubMed Web of Science ®Google Scholar
• Korb, O., Monecke, P., Hessler, G., Stützle, T., & Exner, T. E. (2010). pharmACOphore: Multiple flexible ligand alignment based on ant colony optimization. Journal of Chemical Information and Modeling, 50(9), 1669–1681. doi:10.1021/ci1000218
   PubMed Web of Science ®Google Scholar
• Lajin, B., & Alachkar, A. (2013). The NQO1 polymorphism C609T (Pro187Ser) and cancer susceptibility: A comprehensive meta-analysis. British Journal of Cancer, 109(5), 1325–1337. doi:10.1038/bjc.2013.357
   PubMed Web of Science ®Google Scholar
• Lewis, A. M., Ough, M., Hinkhouse, M. M., Tsao, M.-S., Oberley, L. W., & Cullen, J. J. (2005). Targeting NAD(P)H: Quinone oxidoreductase (NQO1) in pancreatic cancer. Molecular Carcinogenesis, 43(4), 215–224. doi:10.1002/mc.20107
   PubMed Web of Science ®Google Scholar
• Lewis, S. J., Cherry, N. M., Niven, R. M., Barber, P. V., & Povey, A. C. (2001). Polymorphisms in the NAD(P)H: Quinone oxidoreductase gene and small cell lung cancer risk in a UK population. Lung Cancer, 34(2), 177–183. http://doi.org/10.1016/S0169-5002(01)00243-4 doi:10.1016/S0169-5002(01)00243-4
   PubMed Web of Science ®Google Scholar
• Lin, P., Wang, H.-J., & Lee, H. S. (1999). NAD(P)H: Quinone oxidoreductase polymorphism and lung cancer in Taiwan. Journal of Toxicology and Environmental Health, Part A, 58(4), 187–197. http://doi.org/10.1080/009841099157287
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. http://doi.org/10.1016/S0169-409X(96)00423-1 doi:10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• Logsdon, C. D., Simeone, D. M., Binkley, C., Arumugam, T., Greenson, J. K., Giordano, T. J., … Hanash, S. (2003). Molecular profiling of pancreatic adenocarcinoma and chronic pancreatitis identifies multiple genes differentially regulated in pancreatic cancer. Cancer Research, 63(10), 2649–2657.
   PubMed Web of Science ®Google Scholar
• López-Lira, C., Alzate-Morales, J. H., Paulino, M., Mella-Raipán, J., Salas, C. O., Tapia, R. A., & Soto-Delgado, J. (2018). Combined molecular modelling and 3D-QSAR study for understanding the inhibition of NQO1 by heterocyclic quinone derivatives. Chemical Biology & Drug Design, 91(1), 29–38. doi:10.1111/cbdd.13051
   PubMed Web of Science ®Google Scholar
• Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006). Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. Journal of Medicinal Chemistry, 49(16), 4805–4808. doi:10.1021/jm060522a
   PubMed Web of Science ®Google Scholar
• Ma, Y., Kong, J., Yan, G., Ren, X., Jin, D., Jin, T., … Lin, Z. (2014). NQO1 overexpression is associated with poor prognosis in squamous cell carcinoma of the uterine cervix. BMC Cancer, 14(1), 414. doi:10.1186/1471-2407-14-414
   PubMedGoogle Scholar
• Maragakis, P., Lindorff-Larsen, K., Eastwood, M. P., Dror, R. O., Klepeis, J. L., Arkin, I. T., … Shaw, D. E. (2008). Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. The Journal of Physical Chemistry B, 112(19), 6155–6158. doi:10.1021/jp077018h
   PubMed Web of Science ®Google Scholar
• Menzel, H.-J., Sarmanova, J., Soucek, P., Berberich, R., Grünewald, K., Haun, M., & Kraft, H.-G. (2004). Association of NQO1 polymorphism with spontaneous breast cancer in two independent populations. British Journal of Cancer, 90(10), 1989–1994. doi:10.1038/sj.bjc.6601779
   PubMed Web of Science ®Google Scholar
• Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. doi:10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Moscovitz, O., Tsvetkov, P., Hazan, N., Michaelevski, I., Keisar, H., Ben-Nissan, G., … Sharon, M. (2012). A mutually inhibitory feedback loop between the 20S proteasome and its regulator, NQO1. Molecular Cell, 47(1), 76–86. doi:10.1016/j.molcel.2012.05.049
   PubMed Web of Science ®Google Scholar
• Narkhede, S. S., & Degani, M. S. (2007). Pharmacophore refinement and 3D-QSAR studies of histamine H3 antagonists. QSAR & Combinatorial Science, 26(6), 744–753. doi:10.1002/qsar.200610144
   Google Scholar
• Nioi, P., & Hayes, J. D. (2004). Contribution of NAD(P)H:quinone oxidoreductase 1 to protection against carcinogenesis, and regulation of its gene by the Nrf2 basic-region leucine zipper and the arylhydrocarbon receptor basic helix-loop-helix transcription factors. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 555(1-2), 149–171. doi:10.1016/j.mrfmmm.2004.05.023
   PubMed Web of Science ®Google Scholar
• Nolan, K. A., Timson, D. J., Stratford, I. J., & Bryce, R. A. (2006). In silico identification and biochemical characterization of novel inhibitors of NQO1. Bioorganic & Medicinal Chemistry Letters, 16(24), 6246–6254. doi:10.1016/j.bmcl.2006.09.015
   PubMed Web of Science ®Google Scholar
• Oh, E.-T., Kim, J., Kim, J. M., Kim, S. J., Lee, J.-S., Hong, S.-S., … Park, H. J. (2016). NQO1 inhibits proteasome-mediated degradation of HIF-1α. Nature Communications, 7, 13593. http://doi.org/10.1038/ncomms13593
   PubMed Web of Science ®Google Scholar
• Parkinson, E. I., & Hergenrother, P. J. (2015). Deoxynyboquinones as NQO1-activated cancer therapeutics. Accounts of Chemical Research, 48(10), 2715–2723. doi:10.1021/acs.accounts.5b00365
   PubMed Web of Science ®Google Scholar
• Peng, Q., Lu, Y., Lao, X., Chen, Z., Li, R., Sui, J., … Li, S. (2014). The NQO1 Pro187Ser polymorphism and breast cancer susceptibility: Evidence from an updated meta-analysis. Diagnostic Pathology, 9(1), 100. doi:10.1186/1746-1596-9-100
   PubMedGoogle Scholar
• Ramakrishnan, C., Mary Thangakani, A., Velmurugan, D., Anantha Krishnan, D., Sekijima, M., Akiyama, Y., & Gromiha, M. M. (2018). Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques. Journal of Biomolecular Structure and Dynamics, 36(6), 1566–1576. doi:10.1080/07391102.2017.1329098
   PubMed Web of Science ®Google Scholar
• Ross, D., Beall, H. D., Siegel, D., Traver, R. D., & Gustafson, D. L. (1996). Enzymology of bioreductive drug activation. The British Journal of Cancer, 27, S1–S8.
   Google Scholar
• Ross, D., Kepa, J. K., Winski, S. L., Beall, H. D., Anwar, A., & Siegel, D. (2000). NAD(P)H:quinone oxidoreductase 1 (NQO1): Chemoprotection, bioactivation, gene regulation and genetic polymorphisms. Chemico-Biological Interactions, 129(1-2), 77–97. http://doi.org/10.1016/S0009-2797(00)00199-X doi:10.1016/S0009-2797(00)00199-X
   PubMed Web of Science ®Google Scholar
• Sakthivel, S., Habeeb, S. K. M., & Raman, C. (2018). Combined pharmacophore, virtual screening and molecular dynamics studies to identify Bruton’s tyrosine kinase inhibitors. Journal of Biomolecular Structure and Dynamics, 3, 1–18. http://doi.org/10.1080/07391102.2017.1415821
   Google Scholar
• Schlager, J. J., & Powis, G. (1990). Cytosolic NAD(P)H:(quinone-acceptor)oxidoreductase in human normal and tumor tissue: Effects of cigarette smoking and alcohol. International Journal of Cancer, 45(3), 403–409. doi:10.1002/ijc.2910450304
   PubMed Web of Science ®Google Scholar
• Schrödinger, LLC. (2014). QikProp. Schrödinger release 2014-2. New York, NY: Schrödinger, LLC.
   Google Scholar
• Scott, K. A., Barnes, J., Whitehead, R. C., Stratford, I. J., & Nolan, K. A. (2011). Inhibitors of NQO1: Identification of compounds more potent than dicoumarol without associated off-target effects. Biochemical Pharmacology, 81(3), 355–363. doi:10.1016/j.bcp.2010.10.011
   PubMed Web of Science ®Google Scholar
• Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. doi:10.1021/ct900587b
   PubMed Web of Science ®Google Scholar
• Song, S. Y., Jeong, S.-Y., Park, H. J., Park, S.-I., Kim, D. K., Kim, Y. H., … Choi, E. K. (2010). Clinical significance of NQO1 C609T polymorphisms after postoperative radiation therapy in completely resected non-small cell lung cancer. Lung Cancer, 68(2), 278–282. doi:10.1016/j.lungcan.2009.06.009
   PubMed Web of Science ®Google Scholar
• Steindl, T., & Langer, T. (2004). Influenza virus neuraminidase inhibitors: Generation and comparison of structure-based and common feature pharmacophore hypotheses and their application in virtual screening. Journal of Chemical Information and Computer Sciences, 44(5), 1849–1856. doi:10.1021/ci049844i
   PubMedGoogle Scholar
• Tawari, N. R., Bag, S., & Degani, M. S. (2008). Pharmacophore mapping of a series of pyrrolopyrimidines, indolopyrimidines and their congeners as multidrug-resistance-associated protein (MRP1) modulators. Journal of Molecular Modeling, 14(10), 911–921. doi:10.1007/s00894-008-0330-z
   PubMed Web of Science ®Google Scholar
• Tropsha A. (2010). Best Practices for QSAR Model Development, Validation, and Exploitation. Mol Inform, 29(6–7), 476–488. doi:10.1002/minf.201000061.
   Google Scholar
• Verma, P., Tiwari, M., & Tiwari, V. (2018). In silico high-throughput virtual screening and molecular dynamics simulation study to identify inhibitor for AdeABC efflux pump of Acinetobacter baumannii. Journal of Biomolecular Structure and Dynamics, 36(5), 1182–1194. doi:10.1080/07391102.2017.1317025
   PubMed Web of Science ®Google Scholar
• Vijayalakshmi, P., Selvaraj, C., Singh, S. K., Nisha, J., Saipriya, K., & Daisy, P. (2013). Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 31(6), 561–571. doi:10.1080/07391102.2012.706080
   PubMed Web of Science ®Google Scholar
• Wang, H., Aslanian, R., & Madison, V. S. (2008). Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17α pocket flexibility. Journal of Molecular Graphics and Modelling, 27(4), 512–521. doi:10.1016/j.jmgm.2008.09.002
   PubMed Web of Science ®Google Scholar
• Winski, S. L., Faig, M., Bianchet, M. A., Siegel, D., Swann, E., Fung, K., … Ross, D. (2001). Characterization of a mechanism-based inhibitor of NAD(P)H:quinone oxidoreductase 1 by biochemical, X-ray crystallographic, and mass spectrometric approaches. Biochemistry, 40(50), 15135–15142. doi:10.1021/bi011324i
   PubMed Web of Science ®Google Scholar
• Yang, Y., Zhang, Y., Wu, Q., Cui, X., Lin, Z., Liu, S., & Chen, L. (2014). Clinical implications of high NQO1 expression in breast cancers. Journal of Experimental & Clinical Cancer Research, 33(1), 14. doi:10.1186/1756-9966-33-14
   PubMedGoogle Scholar