References
- N. Fujiwara and K. Kobayashi, Macrophages in inflammation, Curr. Drug Targets Inflam. Allergy 4 (2005), pp. 281–286. doi:https://doi.org/10.2174/1568010054022024.
- J.A. Rankin, Biological mediators of acute inflammation, AACN Adv. Crit. Care 15 (2004), pp. 3–17.
- H.B. Cohen and D.M. Mosser, Extrinsic and intrinsic control of macrophage inflammatory responses, J. Leukocyte Biol. 94 (2013), pp. 913–919. doi:https://doi.org/10.1189/jlb.0413236.
- G.M. Barton and R. Medzhitov, Toll-like receptor signaling pathways, Science 300 (2003), pp. 1524–1525. doi:https://doi.org/10.1126/science.1085536.
- I. Sabroe, L.C. Parker, S.K. Dower, and M.K. Whyte, The role of TLR activation in inflammation, J. Pathol. 214 (2008), pp. 126–135. doi:https://doi.org/10.1002/path.2264.
- B. Verstak, K. Nagpal, S.P. Bottomley, D.T. Golenbock, P.J. Hertzog, and A. Mansell, MyD88 adapter-like (Mal)/TIRAP interaction with TRAF6 is critical for TLR2- and TLR4-mediated NF-kappaB proinflammatory responses, J. Biol. Chem. 284 (2009), pp. 24192–24203. doi:https://doi.org/10.1074/jbc.M109.023044.
- L.A. O’Neill and A.G. Bowie, The family of five: TIR-domain-containing adaptors in Toll-like receptor signalling, Nat. Rev. Immunol. 7 (2007), pp. 353–364. doi:https://doi.org/10.1038/nri2079.
- L. Chen, H. Deng, H. Cui, J. Fang, Z. Zuo, J. Deng, Y. Li, X. Wang, and L. Zhao, Inflammatory responses and inflammation-associated diseases in organs, Oncotarget 9 (2018), pp. 7204. doi:https://doi.org/10.18632/oncotarget.23208.
- T. Kawasaki and T. Kawai, Toll-like receptor signaling pathways, Front. Immunol. 5 (2014), pp. 461. doi:https://doi.org/10.3389/fimmu.2014.00461.
- I. Belhaouane, E. Hoffmann, M. Chamaillard, P. Brodin, and A. Machelart, Paradoxical roles of the MAL/Tirap adaptor in pathologies, Front. Immunol. 11 (2020), pp. 569127. doi:https://doi.org/10.3389/fimmu.2020.569127.
- C.A. Jefferies and L.A. O’Neill, Bruton’s tyrosine kinase (Btk)-the critical tyrosine kinase in LPS signalling?, Immunol. Lett. 92 (2004), pp. 15–22. doi:https://doi.org/10.1016/j.imlet.2003.11.017.
- M. Kubo-Murai, K. Hazeki, N. Sukenobu, K. Yoshikawa, K. Nigorikawa, K. Inoue, T. Yamamoto, M. Matsumoto, T. Seya, N. Inoue, and O. Hazeki, Protein kinase Cdelta binds TIRAP/Mal to participate in TLR signaling, Mol. Immunol. 44 (2007), pp. 2257–2264. doi:https://doi.org/10.1016/j.molimm.2006.11.005.
- M. Sakaguchi, H. Murata, K. Yamamoto, T. Ono, Y. Sakaguchi, A. Motoyama, T. Hibino, K. Kataoka, and N.H. Huh, TIRAP, an adaptor protein for TLR2/4, transduces a signal from RAGE phosphorylated upon ligand binding, PLoS One 6 (2011), pp. e23132. doi:https://doi.org/10.1371/journal.pone.0023132.
- S. Rajpoot, K.K. Wary, R. Ibbott, D. Liu, U. Saqib, T.L.M. Thurston, and M.S. Baig, TIRAP in the mechanism of inflammation, Front. Immunol. 12 (2021), pp. 2722. doi:https://doi.org/10.3389/fimmu.2021.697588.
- G. Lopez-Herrera, A. Vargas-Hernandez, M.E. Gonzalez-Serrano, L. Berron-Ruiz, J.C. Rodriguez-Alba, F. Espinosa-Rosales, and L. Santos-Argumedo, Bruton’s tyrosine kinase–an integral protein of B cell development that also has an essential role in the innate immune system, J. Leukocyte Biol. 95 (2014), pp. 243–250. doi:https://doi.org/10.1189/jlb.0513307.
- R.Z. Paracha, A. Ali, J. Ahmad, R. Hussain, U. Niazi, and S.A. Muhammad, Structural evaluation of BTK and PKCdelta mediated phosphorylation of MAL at positions Tyr86 and Tyr106, Comput. Biol. Chem. 51 (2014), pp. 22–35. doi:https://doi.org/10.1016/j.compbiolchem.2014.04.001.
- D.J. Loegering and M.R. Lennartz, Protein kinase C and toll-like receptor signaling, Enzyme Res. 2011 (2011), pp. 537821.
- S.F. Steinberg, Structural basis of protein kinase C isoform function, Physiol. Rev. 88 (2008), pp. 1341–1378. doi:https://doi.org/10.1152/physrev.00034.2007.
- Q. Yang, J.C. Langston, Y. Tang, M.F. Kiani, and L.E. Kilpatrick, The role of tyrosine phosphorylation of protein kinase C delta in infection and inflammation, Int. J. Mol. Sci. 20 (2019) , pp. 1498. doi:https://doi.org/10.3390/ijms20061498.
- P. Gray, A. Dunne, C. Brikos, C.A. Jefferies, S.L. Doyle, and L.A. O’Neill, MyD88 adapter-like (Mal) is phosphorylated by Bruton’s tyrosine kinase during TLR2 and TLR4 signal transduction, J. Biol. Chem. 281 (2006), pp. 10489–10495. doi:https://doi.org/10.1074/jbc.M508892200.
- M.S. Baig, D. Liu, K. Muthu, A. Roy, U. Saqib, A. Naim, S.M. Faisal, M. Srivastava, and R. Saluja, Heterotrimeric complex of p38 MAPK, PKCdelta, and TIRAP is required for AP1 mediated inflammatory response, Int. Immunopharmacol. 48 (2017), pp. 211–218. doi:https://doi.org/10.1016/j.intimp.2017.04.028.
- P. Vignon, P.-F. Laterre, T. Daix, and B. François, New agents in development for sepsis: Any reason for hope? Drugs 80 (2020), pp. 1751–1761. doi:https://doi.org/10.1007/s40265-020-01402-z.
- B. Webb and A. Sali, Protein structure modeling with MODELLER, Methods Mol. Biol. 1654 (2017), pp. 39–54.
- B. Webb and A. Sali, Comparative protein structure modeling using MODELLER, Curr. Protoc. Protein Sci. 86 (2016), pp. 2 9 1–2 9 37. doi:https://doi.org/10.1002/cpps.20.
- J.D. Thompson, T.J. Gibson, and D.G. Higgins, Multiple sequence alignment using ClustalW and ClustalX, Curr. Protoc. Bioinf. (2003), pp. 2.3. 1–2.3. 22.
- R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton, PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26 (1993), pp. 283–291. doi:https://doi.org/10.1107/S0021889892009944.
- C. Colovos and T.O. Yeates, Verification of protein structures: Patterns of nonbonded atomic interactions, Protein Sci. 2 (1993), pp. 1511–1519. doi:https://doi.org/10.1002/pro.5560020916.
- J. Ko, H. Park, L. Heo, and C. Seok, GalaxyWEB server for protein structure prediction and refinement, Nucleic Acids Res. 40 (2012), pp. W294–7. doi:https://doi.org/10.1093/nar/gks493.
- K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, The Swiss-MODEL workspace: A web-based environment for protein structure homology modelling, Bioinformatics 22 (2006), pp. 195–201. doi:https://doi.org/10.1093/bioinformatics/bti770.
- A. Singh, R. Kaushik, A. Mishra, A. Shanker, and B. Jayaram, ProTSAV: A protein tertiary structure analysis and validation server, Biochim. Biophys. Acta 1864 (2016), pp. 11–19. doi:https://doi.org/10.1016/j.bbapap.2015.10.004.
- E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin, UCSF Chimera–a visualization system for exploratory research and analysis, J. Comput. Chem. 25 (2004), pp. 1605–1612. doi:https://doi.org/10.1002/jcc.20084.
- D.S. Biovia, Discovery Studio, Dassault Systemes, San Diego, 2020.
- M.V. Shapovalov and R.L. Dunbrack Jr, A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions, Structure 19 (2011), pp. 844–858. doi:https://doi.org/10.1016/j.str.2011.03.019.
- B. Jimenez-Garcia, C. Pons, and J. Fernandez-Recio, pyDockWEB: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring, Bioinformatics 29 (2013), pp. 1698–1699. doi:https://doi.org/10.1093/bioinformatics/btt262.
- A. Alekseenko, M. Ignatov, G. Jones, M. Sabitova, and D. Kozakov, Protein-protein and protein-peptide docking with ClusPro server, Methods Mol. Biol. 2165 (2020), pp. 157–174.
- S.R. Comeau, D.W. Gatchell, S. Vajda, and C.J. Camacho, ClusPro: A fully automated algorithm for protein-protein docking, Nucleic Acids Res. 32 (2004), pp. W96–W99. doi:https://doi.org/10.1093/nar/gkh354.
- G. Van Zundert, J. Rodrigues, M. Trellet, C. Schmitz, P. Kastritis, E. Karaca, A. Melquiond, M. van Dijk, S. De Vries, and A.J. Bonvin, The HADDOCK2. 2 web server: User-friendly integrative modeling of biomolecular complexes, J. Mol. Biol. 428 (2016), pp. 720–725. doi:https://doi.org/10.1016/j.jmb.2015.09.014.
- T. Sterling and J.J. Irwin, ZINC 15–Ligand discovery for everyone, J. Chem. Inf. Model. 55 (2015), pp. 2324–2337. doi:https://doi.org/10.1021/acs.jcim.5b00559.
- O. Trott and A.J. Olson, AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J. Comput. Chem. 31 (2010), pp. 455–461. doi:https://doi.org/10.1002/jcc.21334.
- B. Hess, C. Kutzner, D. Van Der Spoel, and E. Lindahl, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theor. Comput. 4 (2008), pp. 435–447. doi:https://doi.org/10.1021/ct700301q.
- D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J.C. Berendsen, GROMACS: Fast, flexible, and free, J. Comput. Chem. 26 (2005), pp. 1701–1718. doi:https://doi.org/10.1002/jcc.20291.
- K. Lindorff‐Larsen, S. Piana, K. Palmo, P. Maragakis, J.L. Klepeis, R.O. Dror, and D.E. Shaw, Improved side‐chain torsion potentials for the Amber ff99SB protein force field, Proteins 78 (2010), pp. 1950–1958. doi:https://doi.org/10.1002/prot.22711.
- A.W.S. Da Silva and W.F. Vranken, ACPYPE-Antechamber python parser interface, BMC Res. Notes 5 (2012), pp. 1–8. doi:https://doi.org/10.1186/1756-0500-5-1.
- W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983), pp. 926–935. doi:https://doi.org/10.1063/1.445869.
- P.J. Turner, XMGRACE, Version 5.1. 19, Center for Coastal and Land-Margin Research, Oregon Graduate Institute of Science and Technology, Beaverton, OR, 2005.
- M. Johnson, I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. McGinnis, and T.L. Madden, NCBI BLAST: A better web interface, Nucleic Acids Res. 36 (2008), pp. W5–W9. doi:https://doi.org/10.1093/nar/gkn201.
- P.W. Rose, B. Beran, C. Bi, W.F. Bluhm, D. Dimitropoulos, D.S. Goodsell, A. Prlic, M. Quesada, G.B. Quinn, J.D. Westbrook, J. Young, B. Yukich, C. Zardecki, H.M. Berman, and P.E. Bourne, The RCSB protein data bank: Redesigned web site and web services, Nucleic Acids Res. 39 (2011), pp. D392–D401. doi:https://doi.org/10.1093/nar/gkq1021.
- P. Larsson, B. Wallner, E. Lindahl, and A. Elofsson, Using multiple templates to improve quality of homology models in automated homology modeling, Protein Sci. 17 (2008), pp. 990–1002. doi:https://doi.org/10.1110/ps.073344908.
- S. Chakravarty, S. Godbole, B. Zhang, S. Berger, and R. Sanchez, Systematic analysis of the effect of multiple templates on the accuracy of comparative models of protein structure, BMC Struct. Biol. 8 (2008), pp. 31. doi:https://doi.org/10.1186/1472-6807-8-31.
- J. Cheng, A multi-template combination algorithm for protein comparative modeling, BMC Struct. Biol. 8 (2008), pp. 18. doi:https://doi.org/10.1186/1472-6807-8-18.
- N. Fernandez-Fuentes, B.K. Rai, C.J. Madrid-Aliste, J.E. Fajardo, and A. Fiser, Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structurealignments, Bioinformatics 23 (2007), pp. 2558–2565. doi:https://doi.org/10.1093/bioinformatics/btm377.
- P. Benkert, M. Kunzli, and T. Schwede, QMEAN server for protein model quality estimation, Nucleic Acids Res. 37 (2009), pp. W510–W514. doi:https://doi.org/10.1093/nar/gkp322.
- J. Gong, M. Park, and S.F. Steinberg, Cleavage alters the molecular determinants of protein kinase C-delta catalytic activity, Mol. Cell Biol. 37 (2017). doi:https://doi.org/10.1128/MCB.00324-17.
- J.C. Kagan and R. Medzhitov, Phosphoinositide-mediated adaptor recruitment controls Toll-like receptor signaling, Cell 125 (2006), pp. 943–955. doi:https://doi.org/10.1016/j.cell.2006.03.047.
- Z. Lin, J. Lu, W. Zhou, and Y. Shen, Structural insights into TIR domain specificity of the bridging adaptor Mal in TLR4 signaling, PLoS One 7 (2012), pp. e34202. doi:https://doi.org/10.1371/journal.pone.0034202.
- A. Fiser and A. Sali, ModLoop: Automated modeling of loops in protein structures, Bioinformatics 19 (2003), pp. 2500–2501. doi:https://doi.org/10.1093/bioinformatics/btg362.
- W. Piao, C. Song, H. Chen, L.M. Wahl, K.A. Fitzgerald, L.A. O’Neill, and A.E. Medvedev, Tyrosine phosphorylation of MyD88 adapter-like (Mal) is critical for signal transduction and blocked in endotoxin tolerance, J. Biol. Chem. 283 (2008), pp. 3109–3119. doi:https://doi.org/10.1074/jbc.M707400200.
- T. Kurosaki and M.J. Kurosaki, Transphosphorylation of Bruton’s tyrosine kinase on tyrosine 551 is critical for B cell antigen receptor function, J. Biol. Chem. 272 (1997), pp. 15595–15598. doi:https://doi.org/10.1074/jbc.272.25.15595.
- C. Mao, M. Zhou, and F.M. Uckun, Crystal structure of Bruton’s tyrosine kinase domain suggests a novel pathway for activation and provides insights into the molecular basis of X-linked agammaglobulinemia, J. Biol. Chem. 276 (2001), pp. 41435–41443. doi:https://doi.org/10.1074/jbc.M104828200.
- G. Weng, E. Wang, Z. Wang, H. Liu, F. Zhu, D. Li, and T. Hou, HawkDock: A web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA, Nucleic Acids Res. 47 (2019), pp. W322–W330. doi:https://doi.org/10.1093/nar/gkz397.
- E. Krissinel and K.J. Henrick, Protein interfaces, surfaces and assemblies service PISA at European Bioinformatics Institute, J. Mol. Biol. 372 (2007), pp. 774–797. doi:https://doi.org/10.1016/j.jmb.2007.05.022.
- I. Kronfeld, G. Kazimirsky, P.S. Lorenzo, S.H. Garfield, P.M. Blumberg, and C. Brodie, Phosphorylation of protein kinase Cdelta on distinct tyrosine residues regulates specific cellular functions, J. Biol. Chem. 275 (2000), pp. 35491–35498. doi:https://doi.org/10.1074/jbc.M005991200.
- C.A. Jefferies, S. Doyle, C. Brunner, A. Dunne, E. Brint, C. Wietek, E. Walch, T. Wirth, and L.A. O’Neill, Bruton’s tyrosine kinase is a Toll/interleukin-1 receptor domain-binding protein that participates in nuclear factor kappaB activation by Toll-like receptor 4, J. Biol. Chem. 278 (2003), pp. 26258–26264. doi:https://doi.org/10.1074/jbc.M301484200.
- J.E. Cortes, H. Kantarjian, N.P. Shah, D. Bixby, M.J. Mauro, I. Flinn, T. O’Hare, S. Hu, N.I. Narasimhan, V.M. Rivera, T. Clackson, C.D. Turner, F.G. Haluska, B.J. Druker, M.W.N. Deininger, and M. Talpaz, Ponatinib in refractory Philadelphia chromosome–positive leukemias, N. Engl. J. Med. 367 (2012), pp. 2075–2088. doi:https://doi.org/10.1056/NEJMoa1205127.
- M. Ren, M. Hong, G. Liu, H. Wang, V. Patel, P. Biddinger, J. Silva, J. Cowell, and Z. Hao, Novel FGFR inhibitor ponatinib suppresses the growth of non-small cell lung cancer cells overexpressing FGFR1, Oncol. Rep. 29 (2013), pp. 2181–2190. doi:https://doi.org/10.3892/or.2013.2386.
- T. O’Hare, W.C. Shakespeare, X. Zhu, C.A. Eide, V.M. Rivera, F. Wang, L.T. Adrian, T. Zhou, W.-S. Huang, and Q.J. Xu, AP24534, a pan-BCR-ABL inhibitor for chronic myeloid leukemia, potently inhibits the T315I mutant and overcomes mutation-based resistance, Cancer Cell 16 (2009), pp. 401–412. doi:https://doi.org/10.1016/j.ccr.2009.09.028.
- M. Aapro, A. Carides, B.L. Rapoport, H.-J. Schmoll, L. Zhang, and D.J. Warr, Aprepitant and fosaprepitant: A 10-year review of efficacy and safety, Immunity 20 (2015), pp. 450.
- S. Grunberg, D. Chua, A. Maru, J. Dinis, S. DeVandry, J.A. Boice, J.S. Hardwick, E. Beckford, A. Taylor, and A.J. Carides, Single-dose fosaprepitant for the prevention of chemotherapy-induced nausea and vomiting associated with cisplatin therapy: Randomized, double-blind study protocol—EASE, Am. J. Clin. Oncol. 29 (2011), pp. 1495–1501. doi:https://doi.org/10.1200/JCO.2010.31.7859.
- F.M. Sacks, M. Stanesa, and R.A. Hegele, Severe hypertriglyceridemia with pancreatitis: Thirteen years’ treatment with lomitapide, JAMA Intern. Med. 174 (2014), pp. 443–447. doi:https://doi.org/10.1001/jamainternmed.2013.13309.
- A. Timm and J.M. Kolesar, Crizotinib for the treatment of non-small-cell lung cancer, Am. J. Health Syst. Pharm. 70 (2013), pp. 943–947. doi:https://doi.org/10.2146/ajhp120261.
- Y.-J. Zhang, L. Zhang, S.-B. Wang, -H.-H. Shen, and E.Q. Wei, Montelukast modulates lung CysLT1 receptor expression and eosinophilic inflammation in asthmatic mice, Acta Pharmacol. Sin. 25 (2004), pp. 1341–1346.
- R.A. Duffy, C. Morgan, R. Naylor, G.A. Higgins, G.B. Varty, J.E. Lachowicz, and E.M. Parker, Rolapitant (SCH 619734): A potent, selective and orally active neurokinin NK1 receptor antagonist with centrally-mediated antiemetic effects in ferrets, Pharmacol. Biochem. Behav. 102 (2012), pp. 95–100. doi:https://doi.org/10.1016/j.pbb.2012.03.021.
- C. Owen, N.L. Berinstein, A. Christofides, and L.H. Sehn, Review of Bruton tyrosine kinase inhibitors for the treatment of relapsed or refractory mantle cell lymphoma, Curr. Oncol. 26 (2019), pp. e233–e240. doi:https://doi.org/10.3747/co.26.4345.
- S.P. Soltoff, Rottlerin: An inappropriate and ineffective inhibitor of PKCdelta, Trends Pharmacol. Sci. 28 (2007), pp. 453–458. doi:https://doi.org/10.1016/j.tips.2007.07.003.
- P.J. Wermuth, S. Addya, and S.A. Jimenez, Effect of protein kinase C delta (PKC-delta) inhibition on the transcriptome of normal and systemic sclerosis human dermal fibroblasts in vitro, PLoS One 6 (2011), pp. e27110. doi:https://doi.org/10.1371/journal.pone.0027110.
- D. Mochly-Rosen, K. Das, and K.V. Grimes, Protein kinase C, an elusive therapeutic target?, Nat. Rev. Drug Discov. 11 (2012), pp. 937–957. doi:https://doi.org/10.1038/nrd3871.
- J. Rodrigues, A.S.J. Melquiond, E. Karaca, M. Trellet, M. Van Dijk, G.C.P. Van Zundert, C. Schmitz, S.J. De Vries, A. Bordogna, and L. Bonati, Defining the limits of homology modeling in information‐driven protein docking, Proteins 81 (2013), pp. 2119–2128. doi:https://doi.org/10.1002/prot.24382.