Analysis of Pleurotin binding to human thioredoxin reductase using docking and molecular dynamics simulation

References

• Arnér, E. S., & Holmgren, A. (2000). Physiological functions of thioredoxin and thioredoxin reductase. European Journal of Biochemistry, 267(20), 6102–6109. https://doi.org/10.1046/j.1432-1327.2000.01701.x
   PubMedGoogle Scholar
• Arnér, E. S., & Holmgren, A. (2006). The thioredoxin system in cancer. Seminars in Cancer Biology, 16(6), 420–426. https://doi.org/10.1016/j.semcancer.2006.10.009
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Burke-Gaffney, A., Callister, M. E., & Nakamura, H. (2005). Thioredoxin: Friend or foe in human disease? Trends in Pharmacological Sciences, 26(8), 398–404. https://doi.org/10.1016/j.tips.2005.06.005
   PubMed Web of Science ®Google Scholar
• Cai, W., Zhang, L., Song, Y., Wang, B., Zhang, B., Cui, X., Hu, G., Liu, Y., Wu, J., & Fang, J. (2012). Small molecule inhibitors of mammalian thioredoxin reductase. Free Radical Biology & Medicine, 52(2), 257–265. https://doi.org/10.1016/j.freeradbiomed.2011.10.447
   PubMed Web of Science ®Google Scholar
• Case, D. A., Betz, R. M., Cerutti, D. S., & Kollman, P. A. (2016). AMBER 2016. University of California.
   Google Scholar
• De Souza Pereira, C., Costa Quadros, H., Magalhaes Moreira, D. R., Castro, W., Santos De Deus Da Silva, R. I., Botelho Pereira Soares, M., Fontinha, D., Prudêncio, M., Schmitz, V., Dos Santos, H. F., Gendrot, M., Fonta, I., Mosnier, J., Pradines, B., & Navarro, M. (2021). A Novel Hybrid of Chloroquine and Primaquine Linked by Gold(I): Multitarget and Multiphase Antiplasmodial Agent. ChemMedChem, 16(4), 662–678. https://doi.org/10.1002/cmdc.202000653
   PubMed Web of Science ®Google Scholar
• Dewar, M. J. S., Zoebisch, E. G., Healy, E. F., & Stewart, J. J. P. (1985). Development and use of quantum mechanical molecular models. 76. AM1: A new general purpose quantum mechanical molecular model. Journal of the American Chemical Society, 107(13), 3902–3909. https://doi.org/10.1021/ja00299a024
   Web of Science ®Google Scholar
• Dos Santos, H. F. (2014). Reactivity of auranofin with S-, Se- and N-containing amino acids. Computational and Theoretical Chemistry, 1048, 95–101. https://doi.org/10.1016/j.comptc.2014.09.005
   Web of Science ®Google Scholar
• Engman, L., Al-Maharik, N., McNaughton, M., Birmingham, A., & Powis, G. (2003). Thioredoxin reductase and cancer cell growth inhibition by organotellurium compounds that could be selectively incorporated into tumor cells. Bioorganic & Medicinal Chemistry, 11(23), 5091–5100. https://doi.org/10.1016/j.bmc.2003.08.021
   PubMed Web of Science ®Google Scholar
• Fang, J., Lu, J., & Holmgren, A. (2005). Thioredoxin reductase is irreversibly modified by curcumin: A novel molecular mechanism for its anticancer activity. The Journal of Biological Chemistry, 280(26), 25284–25290. https://doi.org/10.1074/jbc.M414645200
   PubMed Web of Science ®Google Scholar
• Felix, L., Mylonakis, E., & Fuchs, B. B. (2021). Thioredoxin Reductase Is a Valid Target for Antimicrobial Therapeutic Development Against Gram-Positive Bacteria. Frontiers in Microbiology, 12, 663481. https://doi.org/10.3389/fmicb.2021.663481
   PubMed Web of Science ®Google Scholar
• Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G. A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J. E., Hratchian, H. P., Cross, J. B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R. E., Yazyev, O., Austin, A. J., Cammi, R., Pomelli, C., Ochterski, J. W., Ayala, P. Y., Morokuma, K., Voth, G. A., Salvador, P., Dannenberg, J. J., Zakrzewski, V. G., Dapprich, S., Daniels, A. D., Strain, M. C., Farkas, O., Malick, D. K., Rabuck, A. D., Raghavachari, K., Foresman, J. B., Ortiz, J. V., Cui, Q., Baboul, A. G., Clifford, S., Cioslowski, J., Stefanov, B. B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R. L., Fox, D. J., Keith, T., Al-Laham, M. A., Peng, C. Y., Nanayakkara, A., Challacombe, M., Gill, P. M. W., Johnson, B., Chen, W., Wong, M. W., Gonzalez, C., … Pople, J. A. (2004). Gaussian 03, Revision C.02, Gaussian, Inc.,
   Google Scholar
• Fritz-Wolf, K., Urig, S., & Becker, K. (2007). The structure of human thioredoxin reductase 1 provides insights into C-terminal rearrangements during catalysis. Journal of Molecular Biology, 370(1), 116–127. https://doi.org/10.1016/j.jmb.2007.04.044
   PubMed Web of Science ®Google Scholar
• Fritz-Wolf, K., Urig, S., & Becker, K. (2007). X-Ray Structure of Human Thioredoxin Reductase 1, https://doi.org/10.2210/pdb2J3N/pdb
   Google Scholar
• Garcia, A., Machado, R. C., Grazul, R. M., Lopes, M. T., Corrêa, C. C., Dos Santos, H. F., de Almeida, M. V., & Silva, H. (2016). Novel antitumor adamantane-azole gold(I) complexes as potential inhibitors of thioredoxin reductase. Journal of Biological Inorganic Chemistry: JBIC: A Publication of the Society of Biological Inorganic Chemistry, 21(2), 275–292. https://doi.org/10.1007/s00775-016-1338-y
   PubMed Web of Science ®Google Scholar
• He, J., Li, D., Xiong, K., Ge, Y., Jin, H., Zhang, G., Hong, M., Tian, Y., Yin, J., & Zeng, H. (2012). Inhibition of thioredoxin reductase by a novel series of bis-1,2-benzisoselenazol-3(2H)-ones: Organoselenium compounds for cancer therapy. Bioorganic & Medicinal Chemistry, 20(12), 3816–3827. https://doi.org/10.1016/j.bmc.2012.04.033
   PubMed Web of Science ®Google Scholar
• Honorato, R. V., Koukos, P. I., Jiménez-García, B., Tsaregorodtsev, A., Verlato, M., Giachetti, A., Rosato, A., & Bonvin, A. (2021). Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem. Frontiers in Molecular Biosciences, 8, 729513. https://doi.org/10.3389/fmolb.2021.729513
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Jastrząb, A., & Skrzydlewska, E. (2021). Thioredoxin-dependent system: Application of inhibitors. Journal of Enzyme Inhibition and Medicinal Chemistry, 36(1), 362–371. https://doi.org/10.1080/14756366.2020.1867121
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Lata, S., & Akif, M. (2021). Structure-based identification of natural compound inhibitor against M. tuberculosis thioredoxin reductase: Insight from molecular docking and dynamics simulation. Journal of Biomolecular Structure & Dynamics, 39(12), 4480–4489. https://doi.org/10.1080/07391102.2020.1778530
   PubMed Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Miller, B. R., III, McGee, Jr., T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. J. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3332. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Mustacich, D., & Powis, G. (2000). Thioredoxin reductase. )Biochemical Journal, 346Pt 1(1), 1–8. https://doi.org/10.1042/bj3460001
   PubMed Web of Science ®Google Scholar
• Sandargo, B., Thongbai, B., Praditya, D., Steinmann, E., Stadler, M., & Surup, F. (2018). Antiviral 4-Hydroxypleurogrisein and Antimicrobial Pleurotin Derivatives from Cultures of the Nematophagous Basidiomycete Hohenbuehelia grisea. Molecules (Basel, Switzerland), 23(10), 2697. https://doi.org/10.3390/molecules23102697
   PubMed Web of Science ®Google Scholar
• Sharma, M., Khanna, S., Bulusu, G., & Mitra, A. (2009). Comparative modeling of thioredoxin glutathione reductase from Schistosoma mansoni: A multifunctional target for antischistosomal therapy. Journal of Molecular Graphics & Modelling, 27(6), 665–675. https://doi.org/10.1016/j.jmgm.2008.10.009
   PubMed Web of Science ®Google Scholar
• Tavares, T., Azevedo, G., Garcia, A., Carpanez, A., Lewer, P., Paschoal, D., Müller, B., dos Santos, H., Matos, R., Silva, H., Grazul, R., & Fontes, A. (2017). Gold(I) complexes with aryl-thiosemicarbazones: Molecular modeling, synthesis, cytotoxicity and TrxR inhibition. Polyhedron, 132, 95–104. https://doi.org/10.1016/j.poly.2017.05.004
   Web of Science ®Google Scholar
• Teixeira, V. H., Capacho, A. S., & Machuqueiro, M. (2016). The role of electrostatics in TrxR electron transfer mechanism: A computational approach. Proteins, 84(12), 1836–1843. https://doi.org/10.1002/prot.25166
   PubMed Web of Science ®Google Scholar
• Tunes, L. G., Morato, R. E., Garcia, A., Schmitz, V., Steindel, M., Corrêa-Junior, J. D., Dos Santos, H. F., Frézard, F., de Almeida, M. V., Silva, H., Moretti, N. S., de Barros, A., & do Monte-Neto, R. L. (2020). Preclinical Gold Complexes as Oral Drug Candidates to Treat Leishmaniasis Are Potent Trypanothione Reductase Inhibitors. ACS Infectious Diseases, 6(5), 1121–1139. https://doi.org/10.1021/acsinfecdis.9b00505
   PubMed Web of Science ®Google Scholar
• Uberuaga, B. P., Anghel, M., & Voter, A. F. (2004). Synchronization of trajectories in canonical molecular-dynamics simulations: Observation, explanation, and exploitation. The Journal of Chemical Physics, 120(14), 6363–6374. https://doi.org/10.1063/1.1667473
   PubMed Web of Science ®Google Scholar
• Urig, S., & Becker, K. (2006). On the potential of thioredoxin reductase inhibitors for cancer therapy. Seminars in Cancer Biology, 16(6), 452–465. https://doi.org/10.1016/j.semcancer.2006.09.004
   PubMed Web of Science ®Google Scholar
• Vangone, A., & Bonvin, A. M. (2015). Contacts-based prediction of binding affinity in protein-protein complexes. eLife, 4, e07454. https://doi.org/10.7554/eLife.07454
   PubMed Web of Science ®Google Scholar
• Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling, 25(2), 247–260. https://doi.org/10.1016/j.jmgm.2005.12.005
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wipf, P., Hopkins, T. D., Jung, J. K., Rodriguez, S., Birmingham, A., Southwick, E. C., Lazo, J. S., & Powis, G. (2001). New inhibitors of the thioredoxin-thioredoxin reductase system based on a naphthoquinone spiroketal natural product lead. Bioorganic & Medicinal Chemistry Letters, 11(19), 2637–2641. https://doi.org/10.1016/S0960-894X(01)00525-X
   PubMed Web of Science ®Google Scholar
• Wipf, P., Lynch, S. M., Birmingham, A., Tamayo, G., Jiménez, A., Campos, N., & Powis, G. (2004). Natural product based inhibitors of the thioredoxin-thioredoxin reductase system. Organic & Biomolecular Chemistry, 2(11), 1651–1658. https://doi.org/10.1039/b402431a
   PubMed Web of Science ®Google Scholar
• Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford, England), 32(23), 3676–3678. https://doi.org/10.1093/bioinformatics/btw514
   PubMed Web of Science ®Google Scholar
• Zhang, X., Selvaraju, K., Saei, A. A., D'Arcy, P., Zubarev, R. A., Arnér, E. S., & Linder, S. (2019). Repurposing of auranofin: Thioredoxin reductase remains a primary target of the drug. Biochimie, 162, 46–54. https://doi.org/10.1016/j.biochi.2019.03.015
   PubMed Web of Science ®Google Scholar
• Zhang, J., Zhang, B., Li, X., Han, X., Liu, R., & Fang, J. (2019). Small molecule inhibitors of mammalian thioredoxin reductase as potential anticancer agents: An update. Medicinal Research Reviews, 39(1), 5–39. https://doi.org/10.1002/med.21507
   PubMed Web of Science ®Google Scholar