Pathways Knowlegdes

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Pathway DOIs Note
Metabolism

Accession ID: Reactome:R-BTA-1430728		 -
Metabolism of lipids

Accession ID: Reactome:R-BTA-556833		 -
Phase I - Functionalization of compounds

Accession ID: Reactome:R-BTA-211945
  • 10.1208/aapsj080112
  • 10.1517/17425255.2.6.895
  • 10.2174/1389200023337054
 Strolin Benedetti M, Whomsley R, Baltes E. Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics. Expert Opinion on Drug Metabolism & Toxicology. 2006 Nov 24;2(6):895–921. doi: 10.1517/17425255.2.6.895.; Guengerich FP. Cytochrome P450s and other enzymes in drug metabolism and toxicity. The AAPS Journal. 2006 Mar 01;8(1):e101–11. doi: 10.1208/aapsj080112.; Danielson PB. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr Drug Metab. 2002 Dec;3(6):561–97. doi: 10.2174/1389200023337054. PMID: 12369887.
Metabolism

Accession ID: Reactome:R-CFA-1430728		 -
Metabolism of lipids

Accession ID: Reactome:R-CFA-556833		 -
Endogenous sterols

Accession ID: Reactome:R-CFA-211976
  • 10.1016/j.pharmthera.2006.05.014
  • 10.1208/aapsj080112
  • 10.1517/phgs.5.3.305.29827
 Pikuleva IA. Cytochrome P450s and cholesterol homeostasis. Pharmacol Ther. 2006 Dec;112(3):761–73. doi: 10.1016/j.pharmthera.2006.05.014. PMID: 16872679.; Guengerich FP. Cytochrome P450s and other enzymes in drug metabolism and toxicity. The AAPS Journal. 2006 Mar 01;8(1):e101–11. doi: 10.1208/aapsj080112.; Lewis DF. 57 varieties: the human cytochromes P450. Pharmacogenomics. 2004 Apr;5(3):305–18. doi: 10.1517/phgs.5.3.305.29827. PMID: 15102545.
Biological oxidations

Accession ID: Reactome:R-HSA-211859		 -
Disease

Accession ID: Reactome:R-HSA-1643685
  • 10.1002/14651858.cd011076.pub2
  • 10.1002/pro.3936
  • 10.1007/s12272-020-01225-2
  • 10.1007/s40263-014-0155-5
  • 10.1016/0922-4106(93)90072-h
  • 10.1016/j.canlet.2008.04.018
  • 10.1016/j.canlet.2017.10.033
  • 10.1016/j.freeradbiomed.2018.12.033
  • 10.1016/j.msard.2020.102335
  • 10.1021/tx0502138
  • 10.1021/tx100389r
  • 10.1038/ni.1831
  • 10.1038/s41467-020-18764-3
  • 10.1038/s41573-018-0008-x
  • 10.1038/s42003-021-02250-7
  • 10.1073/pnas.0307301101
  • 10.1074/jbc.m000228200
  • 10.1074/jbc.m202196200
  • 10.1083/jcb.200408064
  • 10.1091/mbc.e10-04-0338
  • 10.1101/2021.03.25.437060
  • 10.1111/febs.15485
  • 10.1126/science.279.5350.558
  • 10.1128/mcb.00099-20
  • 10.1128/mcb.23.22.8137-8151.2003
  • 10.1146/annurev.cellbio.22.010305.104219
  • 10.1242/jcs.00500
  • 10.1242/jcs.02528
  • 10.1371/journal.pone.0120254
  • 10.17179/excli2020-2487
  • 10.3727/096504020x15828892654385
 Javorsky A, Humbert PO, Kvansakul M. Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain. Communications Biology. 2021 Jun 11;4(1):724. doi: 10.1038/s42003-021-02250-7.; Ordonez AA, Bullen CK, Villabona-Rueda AF, Thompson EA, Turner ML, Davis SL, Komm O, Powell JD, D'Alessio FR, Yolken RH, Jain SK, Jones-Brando L. Sulforaphane exhibits in vitro and in vivo antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses. bioRxiv. 2021 Mar 25;(). PMID: 33791708; PMCID: PMC8010735.; Olagnier D, Farahani E, Thyrsted J, Blay-Cadanet J, Herengt A, Idorn M, Hait A, Hernaez B, Knudsen A, Iversen MB, Schilling M, Jørgensen SE, Thomsen M, Reinert LS, Lappe M, Hoang H, Gilchrist VH, Hansen AL, Ottosen R, Nielsen CG, Møller C, van der Horst D, Peri S, Balachandran S, Huang J, Jakobsen M, Svenningsen EB, Poulsen TB, Bartsch L, Thielke AL, Luo Y, Alain T, Rehwinkel J, Alcamí A, Hiscott J, Mogensen TH, Paludan SR, Holm CK. Author Correction: SARS-CoV2-mediated suppression of NRF2-signaling reveals potent antiviral and anti-inflammatory activity of 4-octyl-itaconate and dimethyl fumarate. Nature Communications. 2020 Oct 21;11(1):5419. doi: 10.1038/s41467-020-19363-y.; Wynn D, Lategan TW, Sprague TN, Rousseau FS, Fox EJ. Monomethyl fumarate has better gastrointestinal tolerability profile compared with dimethyl fumarate. Multiple Sclerosis and Related Disorders. 2020 Oct;45():102335. doi: 10.1016/j.msard.2020.102335.; Toto A, Ma S, Malagrinò F, Visconti L, Pagano L, Stromgaard K, Gianni S. Comparing the binding properties of peptides mimicking the Envelope protein of SARS-CoV and SARS-CoV-2 to the PDZ domain of the tight junction-associated PALS1 protein. Protein Science. 2020 Sep 08;29(10):2038–42. doi: 10.1002/pro.3936.; Wu G, Yan Y, Zhou Y, Duan Y, Zeng S, Wang X, Lin W, Ou C, Zhou J, Xu Z. Sulforaphane: Expected to Become a Novel Antitumor Compound. oncol res. 2020 Sep 01;28(4):439–46. doi: 10.3727/096504020x15828892654385.; Unni S, Deshmukh P, Krishnappa G, Kommu P, Padmanabhan B. Structural insights into the multiple binding modes of Dimethyl Fumarate (DMF) and its analogs to the Kelch domain of Keap1. FEBS J. 2021 Mar;288(5):1599–613. doi: 10.1111/febs.15485. PMID: 32672401.; Baird L, Yamamoto M. The Molecular Mechanisms Regulating the KEAP1-NRF2 Pathway. Molecular and Cellular Biology. 2020 Jun 15;40(13). doi: 10.1128/mcb.00099-20.; Kamal MM, Akter S, Lin C, Nazzal S. Sulforaphane as an anticancer molecule: mechanisms of action, synergistic effects, enhancement of drug safety, and delivery systems. Archives of Pharmacal Research. 2020 Mar 10;43(4):371–84. doi: 10.1007/s12272-020-01225-2.; McGuinness G, Kim Y. Sulforaphane treatment for autism spectrum disorder: A systematic review. EXCLI J. 2020;19():892–903. PMID: 33013262; PMCID: PMC7527484.; Zhu J, Wang Q, Li C, Lu Y, Hu H, Qin B, Xun Y, Zhu Y, Wu Y, Zhang J, Wang S. Inhibiting inflammation and modulating oxidative stress in oxalate-induced nephrolithiasis with the Nrf2 activator dimethyl fumarate. Free Radic Biol Med. 2019 Apr;134():9–22. doi: 10.1016/j.freeradbiomed.2018.12.033. PMID: 30599261.; Cuadrado A, Rojo AI, Wells G, Hayes JD, Cousin SP, Rumsey WL, Attucks OC, Franklin S, Levonen AL, Kensler TW, Dinkova-Kostova AT. Therapeutic targeting of the NRF2 and KEAP1 partnership in chronic diseases. Nat Rev Drug Discov. 2019 Apr;18(4):295–317. doi: 10.1038/s41573-018-0008-x. PMID: 30610225.; Gründemann C, Huber R. Chemoprevention with isothiocyanates - From bench to bedside. Cancer Lett. 2018 Feb 01;414():26–33. doi: 10.1016/j.canlet.2017.10.033. PMID: 29111351.; Xu Z, Zhang F, Sun F, Gu K, Dong S, He D. Dimethyl fumarate for multiple sclerosis. Cochrane Database Syst Rev. 2015 Apr 22;(4):CD011076. PMID: 25900414; PMCID: PMC10663978.; Brennan MS, Matos MF, Li B, Hronowski X, Gao B, Juhasz P, Rhodes KJ, Scannevin RH. Dimethyl Fumarate and Monoethyl Fumarate Exhibit Differential Effects on KEAP1, NRF2 Activation, and Glutathione Depletion In Vitro. PLoS ONE. 2015 Mar 20;10(3):e0120254. doi: 10.1371/journal.pone.0120254.; Burness CB, Deeks ED. Dimethyl fumarate: a review of its use in patients with relapsing-remitting multiple sclerosis. CNS Drugs. 2014 Apr;28(4):373–87. doi: 10.1007/s40263-014-0155-5. PMID: 24623127.; Hu C, Eggler AL, Mesecar AD, van Breemen RB. Modification of keap1 cysteine residues by sulforaphane. Chem Res Toxicol. 2011 Apr 18;24(4):515–21. PMID: 21391649; PMCID: PMC3086360.; Teoh KT, Siu YL, Chan WL, Schlüter MA, Liu CJ, Peiris JS, Bruzzone R, Margolis B, Nal B. The SARS coronavirus E protein interacts with PALS1 and alters tight junction formation and epithelial morphogenesis. Mol Biol Cell. 2010 Nov 15;21(22):3838–52. PMID: 20861307; PMCID: PMC2982091.; Zhou R, Tardivel A, Thorens B, Choi I, Tschopp J. Thioredoxin-interacting protein links oxidative stress to inflammasome activation. Nat Immunol. 2010 Feb;11(2):136–40. doi: 10.1038/ni.1831. PMID: 20023662.; Clarke JD, Dashwood RH, Ho E. Multi-targeted prevention of cancer by sulforaphane. Cancer Letters. 2008 Oct;269(2):291–304. doi: 10.1016/j.canlet.2008.04.018.; Shin K, Fogg VC, Margolis B. Tight junctions and cell polarity. Annu Rev Cell Dev Biol. 2006;22():207–35. doi: 10.1146/annurev.cellbio.22.010305.104219. PMID: 16771626.; Hong F, Freeman ML, Liebler DC. Identification of sensor cysteines in human Keap1 modified by the cancer chemopreventive agent sulforaphane. Chem Res Toxicol. 2005 Dec;18(12):1917–26. doi: 10.1021/tx0502138. PMID: 16359182.; Michel D, Arsanto JP, Massey-Harroche D, Béclin C, Wijnholds J, Le Bivic A. PATJ connects and stabilizes apical and lateral components of tight junctions in human intestinal cells. J Cell Sci. 2005 Sep 01;118(Pt 17):4049–57. doi: 10.1242/jcs.02528. PMID: 16129888.; Shin K, Straight S, Margolis B. PATJ regulates tight junction formation and polarity in mammalian epithelial cells. J Cell Biol. 2005 Feb 27;168(5):705–11. PMID: 15738264; PMCID: PMC2171825.; Wakabayashi N, Dinkova-Kostova AT, Holtzclaw WD, Kang MI, Kobayashi A, Yamamoto M, Kensler TW, Talalay P. Protection against electrophile and oxidant stress by induction of the phase 2 response: fate of cysteines of the Keap1 sensor modified by inducers. Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):2040–5. PMID: 14764894; PMCID: PMC357048.; Zhang DD, Hannink M. Distinct Cysteine Residues in Keap1 Are Required for Keap1-Dependent Ubiquitination of Nrf2 and for Stabilization of Nrf2 by Chemopreventive Agents and Oxidative Stress. Molecular and Cellular Biology. 2003 Nov 01;23(22):8137–51. doi: 10.1128/mcb.23.22.8137-8151.2003.; Roh MH, Fan S, Liu CJ, Margolis B. The Crumbs3-Pals1 complex participates in the establishment of polarity in mammalian epithelial cells. J Cell Sci. 2003 Jul 15;116(Pt 14):2895–906. doi: 10.1242/jcs.00500. PMID: 12771187.; Lemmers C, Médina E, Delgrossi MH, Michel D, Arsanto JP, Le Bivic A. hINADl/PATJ, a homolog of discs lost, interacts with crumbs and localizes to tight junctions in human epithelial cells. J Biol Chem. 2002 Jul 12;277(28):25408–15. doi: 10.1074/jbc.m202196200. PMID: 11964389.; Lind U, Greenidge P, Gillner M, Koehler KF, Wright A, Carlstedt-Duke J. Functional probing of the human glucocorticoid receptor steroid-interacting surface by site-directed mutagenesis. Gln-642 plays an important role in steroid recognition and binding. J Biol Chem. 2000 Jun 23;275(25):19041–9. doi: 10.1074/jbc.m000228200. PMID: 10747884.; Han J, Luby-Phelps K, Das B, Shu X, Xia Y, Mosteller RD, Krishna UM, Falck JR, White MA, Broek D. Role of substrates and products of PI 3-kinase in regulating activation of Rac-related guanosine triphosphatases by Vav. Science. 1998 Jan 23;279(5350):558–60. doi: 10.1126/science.279.5350.558. PMID: 9438848.; Rupprecht R, Reul JMHM, van Steensel B, Spengler D, Söder M, Berning B, Holsboer F, Damm K. Pharmacological and functional characterization of human mineralocorticoid and glucocorticoid receptor ligands. European Journal of Pharmacology: Molecular Pharmacology. 1993 Oct;247(2):145–54. doi: 10.1016/0922-4106(93)90072-h.
Metabolism

Accession ID: Reactome:R-MMU-1430728		 -
Metabolism of lipids

Accession ID: Reactome:R-MMU-556833		 -
Metabolism of steroids

Accession ID: Reactome:R-MMU-8957322
  • 10.1007/bf00054556
  • 10.1146/annurev.biochem.72.121801.161712
  • 10.1152/ajprenal.00336.2004
  • 10.1194/jlr.r800054-jlr200
  • 10.1210/er.2003-0030
 Brown MS, Goldstein JL. Cholesterol feedback: from Schoenheimer's bottle to Scap's MELADL. Journal of Lipid Research. 2009 Apr;50():S15–27. doi: 10.1194/jlr.r800054-jlr200.; Dusso AS, Brown AJ, Slatopolsky E. Vitamin D. American Journal of Physiology-Renal Physiology. 2005 Jul;289(1):F8–F28. doi: 10.1152/ajprenal.00336.2004.; Payne AH, Hales DB. Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones. Endocr Rev. 2004 Dec;25(6):947–70. doi: 10.1210/er.2003-0030. PMID: 15583024.; Russell DW. The enzymes, regulation, and genetics of bile acid synthesis. Annu Rev Biochem. 2003;72():137–74. doi: 10.1146/annurev.biochem.72.121801.161712. PMID: 12543708.; Russell DW. Cholesterol biosynthesis and metabolism. Cardiovasc Drugs Ther. 1992 Apr;6(2):103–10. doi: 10.1007/bf00054556. PMID: 1390320.
Biological oxidations

Accession ID: Reactome:R-MMU-211859		 -
Metabolism of steroid hormones

Accession ID: Reactome:R-RNO-196071
  • 10.1210/er.2003-0030
 Payne AH, Hales DB. Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones. Endocr Rev. 2004 Dec;25(6):947–70. doi: 10.1210/er.2003-0030. PMID: 15583024.
Phase I - Functionalization of compounds

Accession ID: Reactome:R-RNO-211945
  • 10.1208/aapsj080112
  • 10.1517/17425255.2.6.895
  • 10.2174/1389200023337054
 Strolin Benedetti M, Whomsley R, Baltes E. Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics. Expert Opinion on Drug Metabolism & Toxicology. 2006 Nov 24;2(6):895–921. doi: 10.1517/17425255.2.6.895.; Guengerich FP. Cytochrome P450s and other enzymes in drug metabolism and toxicity. The AAPS Journal. 2006 Mar 01;8(1):e101–11. doi: 10.1208/aapsj080112.; Danielson PB. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr Drug Metab. 2002 Dec;3(6):561–97. doi: 10.2174/1389200023337054. PMID: 12369887.
Metabolism of steroid hormones

Accession ID: Reactome:R-SSC-196071
  • 10.1210/er.2003-0030
 Payne AH, Hales DB. Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones. Endocr Rev. 2004 Dec;25(6):947–70. doi: 10.1210/er.2003-0030. PMID: 15583024.
Phase I - Functionalization of compounds

Accession ID: Reactome:R-SSC-211945
  • 10.1208/aapsj080112
  • 10.1517/17425255.2.6.895
  • 10.2174/1389200023337054
 Strolin Benedetti M, Whomsley R, Baltes E. Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics. Expert Opinion on Drug Metabolism & Toxicology. 2006 Nov 24;2(6):895–921. doi: 10.1517/17425255.2.6.895.; Guengerich FP. Cytochrome P450s and other enzymes in drug metabolism and toxicity. The AAPS Journal. 2006 Mar 01;8(1):e101–11. doi: 10.1208/aapsj080112.; Danielson PB. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr Drug Metab. 2002 Dec;3(6):561–97. doi: 10.2174/1389200023337054. PMID: 12369887.
Cytochrome P450 - arranged by substrate type

Accession ID: Reactome:R-XTR-211897
  • 10.1097/00008571-200401000-00001
  • 10.1208/aapsj080112
  • 10.1517/phgs.5.3.305.29827
  • 10.2174/1389200023337054
 Guengerich FP. Cytochrome P450s and other enzymes in drug metabolism and toxicity. The AAPS Journal. 2006 Mar 01;8(1):e101–11. doi: 10.1208/aapsj080112.; Lewis DF. 57 varieties: the human cytochromes P450. Pharmacogenomics. 2004 Apr;5(3):305–18. doi: 10.1517/phgs.5.3.305.29827. PMID: 15102545.; Nelson DR, Zeldin DC, Hoffman SM, Maltais LJ, Wain HM, Nebert DW. Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants. Pharmacogenetics. 2004 Jan;14(1):1–18. doi: 10.1097/00008571-200401000-00001. PMID: 15128046.; Danielson PB. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr Drug Metab. 2002 Dec;3(6):561–97. doi: 10.2174/1389200023337054. PMID: 12369887.
Metabolism of steroids

Accession ID: Reactome:R-BTA-8957322
  • 10.1007/bf00054556
  • 10.1146/annurev.biochem.72.121801.161712
  • 10.1152/ajprenal.00336.2004
  • 10.1194/jlr.r800054-jlr200
  • 10.1210/er.2003-0030
 Brown MS, Goldstein JL. Cholesterol feedback: from Schoenheimer's bottle to Scap's MELADL. Journal of Lipid Research. 2009 Apr;50():S15–27. doi: 10.1194/jlr.r800054-jlr200.; Dusso AS, Brown AJ, Slatopolsky E. Vitamin D. American Journal of Physiology-Renal Physiology. 2005 Jul;289(1):F8–F28. doi: 10.1152/ajprenal.00336.2004.; Payne AH, Hales DB. Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones. Endocr Rev. 2004 Dec;25(6):947–70. doi: 10.1210/er.2003-0030. PMID: 15583024.; Russell DW. The enzymes, regulation, and genetics of bile acid synthesis. Annu Rev Biochem. 2003;72():137–74. doi: 10.1146/annurev.biochem.72.121801.161712. PMID: 12543708.; Russell DW. Cholesterol biosynthesis and metabolism. Cardiovasc Drugs Ther. 1992 Apr;6(2):103–10. doi: 10.1007/bf00054556. PMID: 1390320.
Biological oxidations

Accession ID: Reactome:R-BTA-211859		 -
Metabolism of steroids

Accession ID: Reactome:R-CFA-8957322
  • 10.1007/bf00054556
  • 10.1146/annurev.biochem.72.121801.161712
  • 10.1152/ajprenal.00336.2004
  • 10.1194/jlr.r800054-jlr200
  • 10.1210/er.2003-0030
 Brown MS, Goldstein JL. Cholesterol feedback: from Schoenheimer's bottle to Scap's MELADL. Journal of Lipid Research. 2009 Apr;50():S15–27. doi: 10.1194/jlr.r800054-jlr200.; Dusso AS, Brown AJ, Slatopolsky E. Vitamin D. American Journal of Physiology-Renal Physiology. 2005 Jul;289(1):F8–F28. doi: 10.1152/ajprenal.00336.2004.; Payne AH, Hales DB. Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones. Endocr Rev. 2004 Dec;25(6):947–70. doi: 10.1210/er.2003-0030. PMID: 15583024.; Russell DW. The enzymes, regulation, and genetics of bile acid synthesis. Annu Rev Biochem. 2003;72():137–74. doi: 10.1146/annurev.biochem.72.121801.161712. PMID: 12543708.; Russell DW. Cholesterol biosynthesis and metabolism. Cardiovasc Drugs Ther. 1992 Apr;6(2):103–10. doi: 10.1007/bf00054556. PMID: 1390320.