Identification of new potent agonists for toll-like receptor 8 by virtual screening methods, molecular dynamics simulation, and MM-GBSA

References

• Alland, C., Moreews, F., Boens, D., Carpentier, M., Chiusa, S., Lonquety, M., Renault, N., Wong, Y., Cantalloube, H., Chomilier, J., Hochez, J., Pothier, J., Villoutreix, B. O., Zagury, J.-F., & Tufféry, P. (2005). RPBS: A web resource for structural bioinformatics. Nucleic Acids Research, 33(Web Server issue), W44–W49. https://doi.org/10.1093/nar/gki477
   PubMedGoogle Scholar
• Arnittali, M., Rissanou, A. N., & Harmandaris, V. (2019). Structure of biomolecules through molecular dynamics simulations. Procedia Computer Science, 156, 69–78. https://doi.org/10.1016/j.procs.2019.08.181
   Google Scholar
• Bitencourt-Ferreira, G., & Azevedo, W. (2019). Molegro virtual Docker for docking. Docking screens for drug discovery (pp. 149–167). Springer.
   Google Scholar
• Burley, S. K., Bhikadiya, C., Bi, C., Bittrich, S., Chen, L., Crichlow, G. V., Christie, C. H., Dalenberg, K., Di Costanzo, L., Duarte, J. M., Dutta, S., Feng, Z., Ganesan, S., Goodsell, D. S., Ghosh, S., Green, R. K., Guranović, V., Guzenko, D., Hudson, B. P., … Zhuravleva, M. (2021). RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Research, 49(D1), D437–D451. https://doi.org/10.1093/nar/gkaa1038
   PubMed Web of Science ®Google Scholar
• Cheng, F., Li, W., Liu, G., & Tang, Y. (2013). In silico ADMET prediction: Recent advances, current challenges and future trends. Current Topics in Medicinal Chemistry, 13(11), 1273–1289. https://doi.org/10.2174/15680266113139990033
   PubMed Web of Science ®Google Scholar
• Chow, L. Q. M., Morishima, C., Eaton, K. D., Baik, C. S., Goulart, B. H., Anderson, L. N., Manjarrez, K. L., Dietsch, G. N., Bryan, J. K., Hershberg, R. M., Disis, M. L., & Martins, R. G. (2017). Phase Ib trial of the toll-like receptor 8 agonist, motolimod (VTX-2337), combined with cetuximab in patients with recurrent or metastatic SCCHN. Clinical Cancer Research, 23(10), 2442–2450. https://doi.org/10.1158/1078-0432.CCR-16-1934
   PubMed Web of Science ®Google Scholar
• Dang, Y., Rutnam, Z. J., Dietsch, G., Lu, H., Yang, Y., Hershberg, R., & Disis, M. L. (2018). TLR8 ligation induces apoptosis of monocytic myeloid‐derived suppressor cells. Journal of Leukocyte Biology, 103(1), 157–164. https://doi.org/10.1002/JLB.5AB0217-070R
   PubMed Web of Science ®Google Scholar
• Gohlke, H., Kiel, C., & Case, D. A. (2003). Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS complexes. Journal of Molecular Biology, 330(4), 891–913. https://doi.org/10.1016/s0022-2836(03)00610-7
   PubMed Web of Science ®Google Scholar
• Gotz, A. W., Williamson, M. J., Xu, D., Poole, D., Le Grand, S., & Walker, R. C. (2012). Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born. Journal of Chemical Theory and Computation, 8(5), 1542–1555. https://doi.org/10.1021/ct200909j
   PubMed Web of Science ®Google Scholar
• Harrach, M. F., & Drossel, B. (2014). Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity. The Journal of Chemical Physics, 140(17), 174501. https://doi.org/10.1063/1.4872239
   PubMed Web of Science ®Google Scholar
• Harvey, M., & De Fabritiis, G. (2009). An implementation of the smooth particle mesh Ewald method on GPU hardware. Journal of Chemical Theory and Computation, 5(9), 2371–2377. https://doi.org/10.1021/ct900275y
   PubMed Web of Science ®Google Scholar
• Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins, 65(3), 712–725. https://doi.org/10.1002/prot.21123
   PubMed Web of Science ®Google Scholar
• Hu, Z., Tanji, H., Jiang, S., Zhang, S., Koo, K., Chan, J., Sakaniwa, K., Ohto, U., Candia, A., Shimizu, T., & Yin, H. (2018). Small-molecule TLR8 antagonists via structure-based rational design. Cell Chemical Biology, 25(10), 1286–1291.e3. https://doi.org/10.1016/j.chembiol.2018.07.004
   PubMed Web of Science ®Google Scholar
• Irwin, J. J., & Shoichet, B. K. (2005). ZINC − a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177–182. https://doi.org/10.1021/ci049714+
   PubMed Web of Science ®Google Scholar
• Kalvakolanu, D. V. (2019). The “Yin-Yang” of cytokines in cancer. Cytokine, 118, 1–2. https://doi.org/10.1016/j.cyto.2018.12.013
   PubMed Web of Science ®Google Scholar
• Karplus, M., & McCammon, J. A. (2002). Molecular dynamics simulations of biomolecules. Nature Structural Biology, 9(9), 646–652. https://doi.org/10.1038/nsb0902-646
   PubMedGoogle Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). BS The PubChem Project. Nucleic Acids Research, 44(D1), D1202–13. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Kumar, V., Patel, S., Tcyganov, E., & Gabrilovich, D. I. (2016). The nature of myeloid-derived suppressor cells in the tumor microenvironment. Trends in Immunology, 37(3), 208–220. https://doi.org/10.1016/j.it.2016.01.004
   PubMed Web of Science ®Google Scholar
• Lagorce, D., Bouslama, L., Becot, J., Miteva, M. A., & Villoutreix, B. O. (2017). FAF-Drugs4: Free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics (Oxford, England), 33(22), 3658–3660. https://doi.org/10.1093/bioinformatics/btx491
   PubMed Web of Science ®Google Scholar
• Lee, T.-S., Cerutti, D. S., Mermelstein, D., Lin, C., LeGrand, S., Giese, T. J., Roitberg, A., Case, D. A., Walker, R. C., & York, D. M. (2018). GPU-accelerated molecular dynamics and free energy methods in Amber18: Performance enhancements and new features. Journal of Chemical Information and Modeling, 58(10), 2043–2050. https://doi.org/10.1021/acs.jcim.8b00462
   PubMed Web of Science ®Google Scholar
• Lester, S. N., & Li, K. (2014). Toll-like receptors in antiviral innate immunity. Journal of Molecular Biology, 426(6), 1246–1264. https://doi.org/10.1016/j.jmb.2013.11.024
   PubMed Web of Science ®Google Scholar
• Lin, Y., Pan, D., Li, J., Zhang, L., & Shao, X. (2017). Application of Berendsen barostat in dissipative particle dynamics for nonequilibrium dynamic simulation. The Journal of Chemical Physics, 146(12), 124108. https://doi.org/10.1063/1.4978807
   PubMed Web of Science ®Google Scholar
• Liu, Y., & Zeng, G. (2012). Cancer and innate immune system interactions: Translational potentials for cancer immunotherapy. Journal of Immunotherapy (Hagerstown, MD: 1997), 35(4), 299–308. https://doi.org/10.1097/CJI.0b013e3182518e83
   PubMed Web of Science ®Google Scholar
• Liu, Z., Xie, Y., Xiong, Y., Liu, S., Qiu, C., Zhu, Z., Mao, H., Yu, M., & Wang, X. (2020). TLR 7/8 agonist reverses oxaliplatin resistance in colorectal cancer via directing the myeloid-derived suppressor cells to tumoricidal M1-macrophages. Cancer Letters, 469, 173–185. https://doi.org/10.1016/j.canlet.2019.10.020
   PubMed Web of Science ®Google Scholar
• McCammon, J. A., Gelin, B. R., & Karplus, M. (1977). Dynamics of folded proteins. Nature, 267(5612), 585–590. https://doi.org/10.1038/267585a0
   PubMed Web of Science ®Google Scholar
• Miu, L., Bogatyreva, N., & Galzitskaia, O. (2008). Radius of gyration is indicator of compactness of protein structure. Molekuliarnaia Biologiia, 42, 701–706.
   PubMed Web of Science ®Google Scholar
• Miyake, K., Shibata, T., Ohto, U., Shimizu, T., Saitoh, S.-I., Fukui, R., & Murakami, Y. (2018). Mechanisms controlling nucleic acid-sensing Toll-like receptors. International Immunology, 30(2), 43–51. https://doi.org/10.1093/intimm/dxy016
   PubMed Web of Science ®Google Scholar
• Monk, B. J., Brady, M. F., Aghajanian, C., Lankes, H. A., Rizack, T., Leach, J., Fowler, J. M., Higgins, R., Hanjani, P., Morgan, M., Edwards, R., Bradley, W., Kolevska, T., Foukas, P., Swisher, E. M., Anderson, K. S., Gottardo, R., Bryan, J. K., Newkirk, M., … Coukos, G. (2017). A phase 2, randomized, double-blind, placebo-controlled study of chemo-immunotherapy combination using motolimod with pegylated liposomal doxorubicin in recurrent or persistent ovarian cancer: A Gynecologic Oncology Group partners study. Annals of Oncology, 28(5), 996–1004. https://doi.org/10.1093/annonc/mdx049
   PubMed Web of Science ®Google Scholar
• Ohto, U., Tanji, H., & Shimizu, T. (2014). Structure and function of toll-like receptor 8. Microbes and Infection, 16(4), 273–282. https://doi.org/10.1016/j.micinf.2014.01.007
   PubMed Web of Science ®Google Scholar
• Pearson, W. R. (2001). Training for bioinformatics and computational biology. Bioinformatics (Oxford, England), 17(9), 761–762. https://doi.org/10.1093/bioinformatics/17.9.761
   PubMed Web of Science ®Google Scholar
• Rakoff-Nahoum, S., & Medzhitov, R. (2009). Toll-like receptors and cancer. Nature Reviews. Cancer, 9(1), 57–63. https://doi.org/10.1038/nrc2541
   PubMed Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E. III (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Schiller, J. T., & Lowy, D. R. (2014). Virus infection and human cancer: An overview. Viruses and Human Cancer, 193, 1–10. http://doi.org/10.1007/978-3-642-38965-8_1
   Google Scholar
• Schnare, M., Barton, G. M., Holt, A. C., Takeda, K., Akira, S., & Medzhitov, R. (2001). Toll-like receptors control activation of adaptive immune responses. Nature Immunology, 2(10), 947–950. https://doi.org/10.1038/ni712
   PubMed Web of Science ®Google Scholar
• Sunseri, J., & Koes, D. R. (2016). Pharmit: Interactive exploration of chemical space. Nucleic Acids Research, 44(W1), W442–W448. https://doi.org/10.1093/nar/gkw287
   PubMed Web of Science ®Google Scholar
• Takeuchi, O., & Akira, S. (2009). Innate immunity to virus infection. Immunological Reviews, 227(1), 75–86. https://doi.org/10.1111/j.1600-065X.2008.00737.x
   PubMed Web of Science ®Google Scholar
• Tanji, H., Ohto, U., Shibata, T., Taoka, M., Yamauchi, Y., Isobe, T., Miyake, K., & Shimizu, T. (2015). Toll-like receptor 8 senses degradation products of single-stranded RNA. Nature Structural & Molecular Biology, 22(2), 109–115. https://doi.org/10.1038/nsmb.2943
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461.
   PubMed Web of Science ®Google Scholar
• Van De Waterbeemd, H., & Gifford, E. (2003). ADMET in silico modelling: Towards prediction paradise? Nature Reviews. Drug Discovery, 2(3), 192–204. https://doi.org/10.1038/nrd1032
   PubMed Web of Science ®Google Scholar
• Vance, R. E., Eichberg, M. J., Portnoy, D. A., & Raulet, D. H. (2017). Listening to each other: Infectious disease and cancer immunology. Science Immunology, 2(7), eaai9339. https://doi.org/10.1126/sciimmunol.aai9339
   PubMed Web of Science ®Google Scholar
• Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z., & Hou, T. (2019). End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
   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
• Wang, X., Chen, Y., Zhang, S., & Deng, J. N. (2022). Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8. PLoS One, 17(4), e0260565. https://doi.org/10.1371/journal.pone.0260565
   PubMed Web of Science ®Google Scholar
• Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20(2), 217–230. https://doi.org/10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
   Web of Science ®Google Scholar
• Zhang, M.-Q., & Wilkinson, B. (2007). Drug discovery beyond the ‘rule-of-five’. Current Opinion in Biotechnology, 18(6), 478–488. https://doi.org/10.1016/j.copbio.2007.10.005
   PubMed Web of Science ®Google Scholar