Thesis Appendix
Creators: name: MohammadiPeyhani Homa
Publisher: name: Zenodo
Year: 2020

description: This appendix contains supplementary tables for the thesis with the title "Developing algorithms and flowcharts for the organization and characterization of synthetic biochemical networks"<br> <strong>List of tables</strong> Table ‎A.4: Strains used in adipic acid bioproduction chapter 5.2. Table A.5: Plasmids used in adipic acid bioproduction chapter 5.2. Table A.6: Biobricks used in adipic acid bioproduction chapter 5.2. Table A.7: Primers used in adipic acid bioproduction chapter 5.2. Table A.8: Heterologous genes discussed in adipic acid bioproduction chapter 5.2. Table A.9: The result of BLASTp algorithm with default settings to align the amino-acid sequence of the large and small subunits of all 121 annotated in KEGG metanogen homoaconitases to <em>Y. lypolytica</em> genome (CLIB122), related to chapter 5.2. Table A.10: Yeast strains used in <em>(S)</em>-tetrahydropalmatine bioproduction in chapter 5.3. Table ‎A.11: Oligonucleotides used in <em>(S)</em>-tetrahydropalmatine bioproduction in chapter 5.3. Table A.12: Genes used in <em>(S)</em>-tetrahydropalmatine bioproduction in chapter 5.3. Table ‎A.13: Plasmids used in <em>(S)</em>-tetrahydropalmatine bioproduction in chapter 5.3. Table ‎A.14: LC-MS/MS multiple reaction monitoring (MRM) transitions and parameters used in <em>(S)</em>-tetrahydropalmatine bioproduction in chapter 5.3. Table ‎A.15: sequences of codon-optimized genes used in <em>(S)</em>-tetrahydropalmatine bioproduction in chapter 5.3. Table A.16: Biochemical network generated by BNICE.ch – COMPOUNDS related to chapter 5.3. Table ‎A.17: Biochemical network generated by BNICE.ch – REACTIONS related to chapter 5.3. Table ‎A.18: Overview on network statistics related to chapter 5.3. Table A.19: Popularity analysis for all BIA compounds in the network, related to chapter 5.3. TableA.20: 50 most popular compounds in the generated network, related to chapter 5.3. Table ‎A.21: Additional information for 15 candidates targets one reaction step away from the initial pathway, related to chapter 5.3. Table ‎A.22: (A) List of cofactors, (B) list of metabolites, and (C) list of E.C. numbers considered in BNICE.ch for the generation of reactions in the analysis of drug metabolism in a human cell, related to chapter 6. Table A.23: Metabolic neighborhood of 5-FU. (1) List of compounds in the 5-FU metabolic neighborhood including up to four reactions or steps away. (2) Description of reactions in the 5-FU metabolic neighborhood including up to four reactions or steps away, related to chapter 6. TableA.24: NICEdrug score between all molecules with reactive site of statins in NICEdrug.ch. Matrix of NICEdrug score between each pair of the whole set of 254 molecules in NICEdrug.ch with reactive site of statins, related to chapter 6. Table ‎A.26: Essential genes or enzymes and linked metabolites in liver-stage Plasmodium and a human cell. (A) List of essential genes and associated reactions in liver-stage Plasmodium, as obtained from the study (Stanway et al., 2019) (B) List of essential genes and associated reactions in a human cell, as obtained from the study (Wang et al., 2015) (C) List of metabolites linked to essential genes in liver-stage Plasmodium. (D) List of metabolites linked to essential genes in a human cell, related to chapter 6. Table ‎A.27: Description of drugs, prodrugs, metabolites and enzymes analyzed in the study of malaria. (A) NICEdrug druggability analysis of essential genes or enzymes in liver-stage Plasmodium: all drugs sharing reactive-site centric similarity with the Plasmodium metabolites and comparison with human metabolites. (B) NICEdrug druggability analysis of essential genes or enzymes in liver-stage Plasmodium: all prodrugs (up to three steps away of 346 drugs) sharing reactive-site centric similarity with the Plasmodium metabolites and comparison with human metabolites. (C) Description of drugs and prodrugs identified in the malaria analysis with NICEdrug.ch and validated in the study by (Antonova-Koch et al., 2018) along with their similar Plasmodium metabolite and human metabolite, related to chapter 6. Table A.28: Hijacked human enzymes by SARS-CoV-2, and drugs and food-based compounds that can inhibit them based on the NICEdrug score. (A) Hijacked human proteins by SARS-CoV-2 as identified by (Gordon et al., 2020) with an annotated enzymatic function (E.C. number), also called here "SARS-CoV-2 hijacked enzymes". (B) NICEdrug druggability report for SARS-CoV-2 hijacked enzymes including all NICEdrug small molecules. (C) Best candidate drugs against COVID-19: NICEdrug druggability report for SARS-CoV-2 hijacked enzymes including drugs with NICEdrug score above 0.5 compared to the native human substrate. (D) Summary of NICEdrug best candidate drugs against COVID-19 and their classification according to the drug category in the KEGG database. (E) NICEdrug druggability report of SARS-CoV-2 hijacked enzymes including prodrugs (up to three steps away of any NICEdrug small molecule) with NICEdrug score above 0.5 compared to the native human substrate. (F) Best candidate food-based molecules against COVID-19: NICEdrug druggability report of SARS-CoV-2 hijacked enzymes including food-based molecules with NICEdrug score above 0.5 compared to the native human substrate. (G) Summary of the NICEdrug best candidate food-based molecules against COVID-19 and their classification according to the fooDB source, related to chapter 6. Table ‎A.29: NICEdrug analysis of inhibitory mechanisms of currently used anti SARS-CoV-2 drugs. (A) All drug molecules and (B) prodrugs in NICEdrug.ch sharing reactive site with the native substrates of the human enzyme HDAC2 and their NICEdrug score with this substrate. (C) All molecules cataloged in fooDB sharing reactive site with the native substrates of the human enzyme HDAC2 and their NICEdrug score with this substrate. (D) All drug molecules and (E) prodrug molecules in NICEdrug.ch sharing reactive site with the native substrates of the human enzyme ACE2 and their NICEdrug score with this substrate. (F) All molecules cataloged in fooDB sharing reactive site with the native substrates of the human enzyme ACE2 and their NICEdrug score with this substrate. (G) All molecules in NICEdrug.ch or cataloged in fooDB sharing reactive site with the native substrates of the human enzyme DNA-directed RNA polymerase and their NICEdrug score with this substrate, related to chapter 6.