SYNTHESIS OF PYRIMIDINE, THIAZINE, DIAZEPINE AND QUINOXALINE DERIVATIVES VIA 3-COMPONENT REACTIONS (3-CR) Reagan Lehlogonolo Mohlala A thesis submitted to the Faculty of Science University of the Witwatersrand, Johannesburg, In fulfilment of the requirements for the degree Doctor of Philosophy April 2021 Supervisors: Prof Moira L Bode Dr E. Mabel Coyanis I, Reagan Lehlogonolo Mohlala student number 795177, declare that the work presented in this thesis was done entirely by myself under the supervision of Prof Moira L. Bode and Dr E. Mabel Coyanis. It is being submitted for the degree of Doctoral philosophy of Science in the University of the Witwatersrand, Johannesburg. It has not been submitted before for any degree or examination in any other University. ___________________ Reagan Lehlogonolo Mohlala student number (795177) July 2021 (Final Submission) iii Abstract Preliminary molecular modeling (virtual screening) in search of bioactive heterocyclic compounds as potential disrupters of HIV-1 integrase and LEDGF/p75 interactions resulted in the identification of fused heterocyclic scaffolds such as hexahydroquinolines, pyrimidines quinoxalines and diazepines. The use of multicomponent reactions (MCRs) for synthesis of heterocyclic scaffolds in synthetic chemistry remains one of the preferred approaches due to atom economy. This thesis describes the use of three-component reactions for the synthesis of fused pyrimidines, thiazines, diazepines and quinoxalines as a strategic approach to accessing these fused heterocycles. The hexahydroquinoline derivatives identified as potential ligands to disrupt the interaction of HIV-1 IN and LEDGF/p75 were chosen for initial synthesis based on availability of reagents and a facile synthetic route. This synthesis resulted in a library of fifteen novel hexahydroquinoline derivatives. The first MCR approach applied involved was 3-CR of isocyanides with electron deficient alkynes (DMAD), giving rise to a zwitterion adduct that was reacted further with a range of prepared five-membered ring substrates containing an acidic proton. The resulting products were 5-6 fused ring heterocycles. When a thiazole derivative was used as a substrate the final racemic products obtained, containing a single stereogenic centre, were (E)-dimethyl 7-(tert- butylamino)-2-(2-methoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H-thiazolo[3,2- a]pyrimidine-5,6-dicarboxylates in good yields. The second five-membered ring substrate used was pyrrolidine which gave dimethyl 2-(tert-butylamino)-6-oxo-4,6,7,8- tetrahydropyrrolo[1,2-a]pyrimidine-3,4-dicarboxylates, also containing one stereogenic centre. Two substrates tested, 1H-1,2,4-triazole-5-thiol and 1H-1,2,4-triazol-5-amine each resulted in formation of two co-products; from a three-component reaction as well as a two- component reaction where the substrate reacted directly with DMAD. Substrate 1H-1,2,4- triazole-5-thiol gave rise to dimethyl 5-(tert-butylamino)-7H-[1,2,4]triazolo[5,1- b][1,3]thiazine-6,7-dicarboxylate and methyl 7-oxo-7H-[1,2,4]triazolo[5,1-b][1,3]thiazine-5- carboxylate while substrate 1H-1,2,4-triazol-5-amine gave rise to dimethyl 5-(tert- butylamino)-6,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidine-6,7-dicarboxylate and methyl 5- oxo-5,8-dihydro-[1,2,4]triazolo[4,3-a]pyrimidine-7-carboxylate. iv The substrate scope of the 3-CR was extended by using six-membered 2-amino-4H-1,3-thiazin- 4-one derivatives to obtain 6-6 fused ring heterocycles. When this set of substrates was treated with zwitterion adducts this resulted in formation of 4-oxo-4,6-dihydropyrimido[2,1- b][1,3]thiazine-6,7-dicarboxylate derivatives, containing one stereogenic centre, in good yields without use of a catalyst. The Michael reaction of prepared five-membered ring substrates with electron deficient alkynes (DMAD\DEtAD\DTAD) gave rise to fused thiazole-pyrimidine derivatives containing no stereogenic centre. When thiazol-2-amine and its derivatives were treated with electron deficient alkynes they gave average yields of methyl 7-oxo-7H-thiazolo[3,2-a]pyrimidine-5- carboxylate derivatives. The alternative route of employing thiourea, α-haloketone and DMAD gave improved yields of the resulting thiazolo[3,2-a]pyrimidine-5-carboxylate derivatives via 3-CR. When DMAD\DEtAD were treated with 1H-1,2,4-triazol-5-amine or 1H-1,2,4-triazole- 5-thiol this resulted in good yields from 2-CR. When 2-imino-1,3-oxazolidine was reacted with DMAD\DEtAD this resulted in a good yield of methyl 5-oxo-3,5-dihydro-2H-oxazolo[3,2- a]pyrimidine-7-carboxylates. The unexpected incorporation of the solvent acetone in reaction with an isocyanide and benzimidazole via 3-CR resulted in fused diazepine scaffolds, 2-methyl-N-(2,2,4-trimethyl- 2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10-ylidene)propan-2-amine derivatives, when using benzimidazole bearing neutral or activating groups on the benzene ring such as hydrogen and methyl. When using deactivating groups on the benzimidazole such as an ester group, reaction with acetone and isocyanide gave quinoxaline scaffolds instead. These reactions occurred without use of solvent or catalyst. The reaction of phenylenediamine or benzimidazole with DMAD\DEtAD\DTAD gave rise to diazepine scaffolds. Various biological studies were conducted on the synthesised compounds, such as antimicrobial Minimum Inhibitory Concentration (MIC) assays for Gram-positive and Gram- negative organisms; antiviral HIV assays which were conducted in infected MT4 cells; cytotoxicity assays which were conducted in the MT4 cell line at 100 μM; and an assay was conducted on certain substrates to test for inhibition or disruption of the HIV-1 IN-LEDGF/p75 protein-protein interaction. v Dedications I dedicate this thesis to my family and close relatives: To my parents Andrew Mohlala, Monica Mohlala To my siblings/close relatives McDonald, Gregory, Tumelo, Onica, Lebo, Phethego, Andria. Little kids and babies: Bakedi, Tswelopele, Kaugelo, Lesedi and Paballo. vi Acknowledgements I would like to extend my sincere gratitude and appreciation to my supervisors Prof Moira L. Bode (University of Witwatersrand) and Dr E. Mabel Coyanis (Mintek) for guidance, support, mentorship, good personality, open discussion and time they had for this study with patience. I would also like to appreciate the quality service and guidance of Prof Manuel Fernandes (University of Witwatersrand) for the Single X-ray crystallography analysis. Thanks to the presence and help of Dr Thompho Jason Rashamuse (Mintek), Dr James Sehata (Mintek) and Biomed group. The following people are acknowledged according to their contribution and effort:  Dr: Qasim Fish: Cytotoxicity, antiviral and antimicrobial studies.  Ms Mapula Makgoba: for antimicrobial studies.  Dr. Angela Harrison: for her help in HIV-1-IN and LEDGF/p75 biological evaluation studies.  Dr Adriaan E. Basson: for antiviral screening. The following Institutions are acknowledged: Mintek, Advanced Material Division AMD, Biomed group School of chemistry at the University of the Witwatersrand National Research Foundation I would also like to thank my research group members at Mintek and Wits, friends and the internal Mintek soccer teams. To my family I would say I was blessed to have all your support and courage through hard and nice times. vii List of abbreviations AlphaScreen: Amplified luminescent proximity pomogeneous assay ADME: Absorption, distribution, metabolism and excretion Al(N3)3: Aluminium azide Al-MCM-41: Aluminium mobil composition of matter No.41 AFIR: Artificial force induced reaction 2-CR: Two-component reactions 3-CR: Three-component reactions 4-CR: Four-component reactions CSA: Camphorsulfonic acid CCD: Catalytic core domain CC50: 50% Cytotoxic concentration CDCl3: Deuterated chloroform CDI: Carbonyldiimidazole DCM: Dichloromethane DDQ: 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone DEtAD: Diethyl acetylenedicarboxylate DHMP: 3,4-Dihydropyrimidin-2(1H)-one DHP: Dihydropyridine DMAD: Dimethyl acetylenedicarboxylate DMF: N,N-Dimethylformamide DMSO-d6: Deuterated dimethyl sulfoxide DTAD: Ditert-butyl acetylenedicarboxylate EtOAc: Ethyl acetate EtOH: Ethanol ESI-LCMS: Electrospray ionization liquid chromatography mass spectrometry ELISA: Enzyme-linked immunosorbent assay FTIR: Fourier transform infrared spectroscopy HRMS: High resolution mass spectrometry HIV-1: Human immunodeficiency virus type-1 h: Hour(s) HN3: Hydrazoic acid IBD: Integrase binding domain viii IMCRs: Isocyanide-based multicomponent reactions IN: Integrase enzyme INT: Iodonitrotetrazolium iPrOH: Isopropanol LDA: Lithium diisopropylamide LEDGF/p75: Lens epithelium-derived growth factor, or transcriptional coactivator MT-4: Metallothionein 4 cell line MeCN: Acetonitrile MeOH: Methanol MIC: Minimum inhibitory concentration Min: Minute(s) MMGBSA: Molecular mechanics/generalized born surface area MCRs: Multicomponent reactions MW: Microwave irradiation NMR: Nuclear magnetic resonance RNAi: Ribonucleic acid interference TEMPO: 2,2,6,6-Tetramethyl-piperidin-1-oxyl THF: Tetrahydrofuran TFE: 2,2,2-Trifluoroethanol TosMIC: p-Toluenesulfonylmethyl isocyanide TLC: Thin layer chromatography TSB: Tryptic soy broth pTsOH: Toluenesulfonic acid Wits: University of the Witwatersrand ix Table of contents ABSTRACT .......................................................................................................................................................... III DEDICATIONS ..................................................................................................................................................... V ACKNOWLEDGEMENTS ..................................................................................................................................... VI LIST OF ABBREVIATIONS .................................................................................................................................. VII TABLE OF CONTENTS ................................................................................................................................................ IX CHAPTER 1 ....................................................................................................................................................... 1 LITERATURE REVIEW ........................................................................................................................................ 1 1.1 INTRODUCTION TO MULTICOMPONENT REACTIONS ................................................................................................... 1 1.2. STRECKER REACTION (S-3CR) ............................................................................................................................. 3 1.3. HANTZSCH REACTION (H-3CR) ........................................................................................................................... 4 1.4. BIGINELLI REACTION (B-3CR) ............................................................................................................................. 5 1.5. PASSERINI REACTION (P-3CR) ............................................................................................................................ 6 1.5.1 Substrate scope in the Passerini reactions ............................................................................................ 9 1.5.2 Chirality in Passerini reactions ............................................................................................................ 11 1.6. UGI REACTION: U-4CR AND U-3CR .................................................................................................................. 14 1.6.1 Ugi-four component reaction (U-4CR) ................................................................................................ 14 1.6.2 Ugi-three component reaction (U-3CR) .............................................................................................. 18 1.7. VAN LEUSEN REACTION (V-3CR) ....................................................................................................................... 20 1.8 THE APPLICATION OF DIMETHYL ACETYLENEDICARBOXYLATE IN ORGANIC SYNTHESIS ...................................................... 21 1.8.1 DMAD and isocyanides in multicomponent reactions ........................................................................ 22 1.8.1.1 Synthesis of heterocyclic scaffolds using zwitterions and nucleophiles containing acidic protons. . 24 1.8.1.2 Synthesis of heterocyclic scaffods using zwitterions and electrophiles ............................................ 27 1.8.2 DMAD in Michael reactions ................................................................................................................ 30 1.8.3 DMAD in cycloaddition reactions ........................................................................................................ 32 1.9. MULTICOMPONENT REACTIONS IN MEDICINAL CHEMISTRY ...................................................................................... 34 1.10 MULTICOMPONENT REACTIONS IN GREEN CHEMISTRY PRACTICE .............................................................................. 38 1.10.1 The Principles of Green Chemistry..................................................................................................... 39 1.10.2 Examples of Green Chemistry in practice .......................................................................................... 40 1.11 THE USE MCRS FOR SYNTHESIS OF NATURAL PRODUCTS ........................................................................................ 41 1.12 RESEARCH BACKGROUND ................................................................................................................................ 46 1.12.1 Project strategy and aims ................................................................................................................. 50 1.12.2 Synthetic approach via MCRs ............................................................................................................ 50 1.12.3 Outline:.............................................................................................................................................. 52 CHAPTER 2 ..................................................................................................................................................... 54 SYNTHESIS OF HIGHLY FUNCTIONALISED HEXAHYDROQUINOLINES USING CDI AS A MEDIATOR ................................................................................................................................................. 54 2.1. INTRODUCTION .............................................................................................................................................. 54 2.2 VIRTUAL SCREENING OF HIV-1 INTEGRASE IN COMPLEX WITH LEDGF/P75 BINDING SITE INHIBITORS ............................. 55 2.2.1 HIV-1 integrase and LEDGF/p75 complex ........................................................................................... 55 x 2.2.2 Ligand preparation .............................................................................................................................. 56 2.2.4 Preparation of HIV-1 IN protein .......................................................................................................... 56 2.2.5 Molecular docking of compounds into the HIV IN binding site ........................................................... 57 2.3 SYNTHETIC ROUTE TOWARD N-(4-CHLOROPHENYL)-7,7-DIMETHYL-2,5-DIOXO-1,2,5,6,7,8-HEXAHYDROQUINOLINE-3- CARBOXAMIDE AND ITS DERIVATIVES ......................................................................................................................... 62 2.3.1 Retrosynthesis of target compounds N-(4-chlorophenyl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8- hexahydroquinoline-3-carboxamides ........................................................................................................... 62 2.4. STEPWISE PREPARATION OF 2,5-DIOXO-1,2,5,6,7,8-HEXAHYDROQUINOLINE-3-CARBOXYLIC ACID INTERMEDIATES (2.6A-B) .......................................................................................................................................................................... 64 2.5. SYNTHESIS OF 7,7-DIMETHYL-2,5-DIOXO-N-PHENYL-1,2,5,6,7,8-HEXAHYDROQUINOLINE-3-CARBOXAMIDE DERIVATIVES 2.8A-M AND 2.10A-D ........................................................................................................................................... 65 2.5.1 The effect of aniline substituents and 4-phenylthiazol-2-amine derivatives on synthesis .................. 68 2.6. THE STRUCTURAL ELUCIDATION OF COMPOUNDS 2.8A-M AND 2.11A-D USING FTIR, NMR AND HRMS ........................ 69 2.7. BIOLOGICAL EVALUATIONS OF LIBRARY OF HEXAHYDROQUINOLINE-3-CARBOXAMIDE 2.8 AND 2.11 DERIVATIVES .............. 71 2.8. CONCLUSION ................................................................................................................................................. 75 CHAPTER 3 ..................................................................................................................................................... 76 SYNTHESIS OF FUSED PYRIMIDINE DERIVATIVES VIA 3-CR USING ZWITTERION ADDUCT AS INTERMEDIATE . 76 3.1 INTRODUCTION ............................................................................................................................................... 76 3.2. PREPARATION OF 5-MEMBERED RING INTERMEDIATES ........................................................................................... 77 3.3 SYNTHESIS OF PYRIMIDINE DERIVATIVES AND THEIR ANALOGUES USING AN ISOCYANIDE-BASED 3-CR. .......................................................................................................................................................................... 79 3.4 STRUCTURAL ELUCIDATION OF PYRIMIDINE DERIVATIVES BY FTIR, NMR, HRMS AND SINGLE X-RAY CRYSTALLOGRAPHY TECHNIQUES ......................................................................................................................................................... 85 3.5 BIOLOGICAL EVALUATION OF LIBRARY OF 5-MEMBERED RING FUSED PYRIMIDINE DERIVATIVES ........................................ 88 3.6. CONCLUSION ................................................................................................................................................. 91 3.7. FUTURE WORK ............................................................................................................................................... 91 CHAPTER 4 ..................................................................................................................................................... 93 A FACILE AND EFFICIENT ONE POT 3-CR METHOD FOR THE SYNTHESIS OF NOVEL THIAZINE-BASED HETEROCYCLIC COMPOUNDS USING ZWITTERION ADDUCT INTERMEDIATES ................................................ 93 4.1 INTRODUCTION ............................................................................................................................................... 93 4.2 PREPARATION OF 2-AMINO-4H-1,3-THIAZIN-4-ONE DERIVATIVES USING ALKYL PROPIOLATE DERIVATIVES AND THIOUREA ... 93 4.2.1 Preparation of 2-amino-4H-1,3-thiazin-4-one derivatives (4.3) using different solvents under reflux. ..................................................................................................................................................................... 94 4.2.2 Preparation of 4.4a-e using different solvents at room temperature ................................................. 96 4.2.3 Preparation of 2-amino-4H-1,3-thiazin-4-one derivatives at 0-5ºC .................................................... 97 4.2.4 The analysis of derivatives 4.3a-e by FTIR and NMR techniques ........................................................ 98 4.3. SYNTHESIS OF DIMETHYL 8-(TERT-BUTYLAMINO)-4-OXO-4,6-DIHYDROPYRIMIDO[2,1-B][1,3]THIAZINE-6,7-DICARBOXYLATE (4.7) DERIVATIVES USING ZWITTERIONIC ADDUCTS ....................................................................................................... 99 4.4 THE STRUCTURAL ELUCIDATION OF DERIVATIVES 4.8A-U BY FTIR, NMR AND HRMS TECHNIQUES ................................ 104 4.5 BIOLOGICAL EVALUATIONS OF THIAZINE DERIVATIVE ............................................................................................. 107 4.6. CONCLUSIONS .............................................................................................................................................. 109 xi 4.7. FUTURE WORK ............................................................................................................................................. 109 CHAPTER 5 ................................................................................................................................................... 111 SYNTHESIS OF FUSED THIAZOLE-PYRIMIDINE DERIVATIVES VIA 2-CR AND 3-CR USING ELECTRON DEFICIENT ALKYNES AS MICHAEL ACCEPTORS............................................................................................................... 111 5.1. INTRODUCTION ............................................................................................................................................ 111 5.2 PREPARATION OF SUBSTRATES 5.3, 5.4, 5.7A-H, 5.8, 5.9A-B, 5.10 AND 5.11A-E.................................................... 113 5.3. SYNTHESIS OF THIAZOLE-PYRIMIDINE DERIVATIVES AND THEIR ANALOGUES VIA 2-CR USING ELECTRON DEFICIENT DIALKYL ACETYLENEDICARBOXYLATES AS MICHAEL ACCEPTORS. ................................................................................................ 115 5.4 SYNTHESIS OF THIAZOLE-PYRIMIDINE DERIVATIVES VIA 3-CR OF THIOUREA, Α-HALOKETONE AND DMAD. ...................... 119 5.5 COMPARISON BETWEEN 2-CR AND 3-CR APPROACH ............................................................................................ 121 5.5.1 Isolated yields of thiazole-pyrimidine derivatives synthesised via 2-CR and 3-CR ............................ 121 5.5.2. Substituent effects on yields when using 2-CR and 3-CR.................................................................. 123 5.6. STRUCTURAL ELUCIDATION OF SYNTHESISED COMPOUNDS USING FTIR, NMR, HRMS AND SINGLE X RAY CRYSTALLOGRAPHY. ............................................................................................................................. 124 5.6.1. The structural analysis of thiazole-pyrimidines 5.17a-o. ................................................................. 124 5.6.2. The structural analysis of oxazolo-pyrimidines 5.18a-b (NMR, FTIR and HRMS) ............................. 125 5.6.3. The structural elucidation of triazolo-thiazine 5.6a-b (NMR, FTIR, HRMS and single X-ray Crystallography) ......................................................................................................................................... 127 5.6.4. The structural analysis of triazolo-pyrimidines 5.5a-b (NMR, FTIR and HRMS) ............................... 127 5.7. BIOLOGICAL EVALUATIONS OF PYRIMIDINES AND THEIR ANALOGUES ........................................................................ 129 5.8. CONCLUSION ............................................................................................................................................... 131 CHAPTER 6 ................................................................................................................................................... 133 CATALYST-FREE AND SOLVENT-FREE REACTIONS FOR THE SYNTHESIS OF DIAZEPINES AND QUINOXALINES VIA ONE POT THREE-COMPONENT REACTION USING BENZIMIDAZOLE, ISOCYANIDES AND KETONES ......... 133 6.1 INTRODUCTION ............................................................................................................................................. 133 6.2 PREPARATION OF BENZIMIDAZOLE DERIVATIVES USING 1,2-PHENYLENEDIAMINES ....................................................... 134 6.2.1 Analysis of 1H-benzo[d]imidazol-2(3H)-one derivatives (6.3a-k) by NMR spectroscopy .................. 136 6.3 UNEXPECTED SYNTHESIS OF DIAZEPINE DERIVATIVES FROM BENZIMIDAZOLES, ISOCYANIDE DERIVATIVES AND ACETONE. ..... 136 6.3.1. The effect of activating and deactivating substituent groups on yield of 6.8a-h ............................ 140 6.3.2 The structure elucidation of 6.8a-h, 6.12a-b and 6.13 by FTIR, NMR, HRMS and X-ray crystallography techniques .................................................................................................................................................. 141 6.4. CATALYST-FREE SYNTHESIS OF NOVEL QUINOXALINE-BASED COMPOUNDS FROM BENZIMIDAZOLES, ISOCYANIDE DERIVATIVES AND ACETONE /3-PENTANONE (6.14A-I) ................................................................................................................. 143 6.4.1 The effect of deactivating substituents on the yield of 6.14a-i. ........................................................ 146 6.4.2 The elucidation of products 6.14a-i by FTIR, NMR, HRMS and Single X-ray Crystallography techniques for 6.14f-g. ............................................................................................................................... 147 6.5 SYNTHESIS OF DIAZEPINES AND QUINOXALINES USING DEUTERATED-ACETONE (ACETONE-D6) ........................................ 150 6.5.1 The effect of acetone-d6 on yield of diazepines 6.8 and quinoxalines 6.14. ..................................... 151 6.5.2 Analysis of deuterated diazepines and quinoxaline derivatives by FTIR, NMR and HRMS ............... 152 6.6 SYNTHESIS OF METHYL 4-OXO-4,5-DIHYDRO-1H-BENZO[B][1,4]DIAZEPINE-2-CARBOXYLATE DERIVATIVES 6.13 FROM DMAD/DETAD/DTAD AND 1,2-PHENYLENEDIAMINES/ BENZIMIDAZOLES. .................................................................. 153 xii 6.6.1. The effect of activating and deactivating groups on synthesis of methyl 4-oxo-4,5-dihydro-1H- benzo[b][1,4]diazepine-2-carboxylate derivatives 6.16 ............................................................................. 155 6.6.2 The structure elucidation of 6.16a-j by FTIR, NMR spectroscopy and HRMS techniques.................. 156 6.7 BIOLOGICAL EVALUATIONS OF DIAZEPINE AND QUINOXALINE DERIVATIVES ................................................................. 158 6.8. CONCLUSIONS .............................................................................................................................................. 159 6.9. FUTURE WORK ............................................................................................................................................. 161 CHAPTER 7 ................................................................................................................................................... 163 GENERAL CONCLUSIONS .............................................................................................................................. 163 7.1 STRATEGY AND APPROACHES EMPLOYED ............................................................................................................ 163 7.2 SYNTHESIS OF HEXAHYDROQUINOLINE COMPOUNDS ............................................................................................. 163 7.3 THE SYNTHESIS OF PYRIMIDINES, THIAZINES AND THEIR ANALOGUES ......................................................................... 166 7.4 SYNTHESIS OF DIAZEPINES AND QUINOXALINES UNDER CATALYST-FREE AND SOLVENT-FREE CONDITIONS, VIA 3-CR. .......... 170 7.5 BIOLOGICAL EVALUATIONS OF ALL NEWLY SYNTHESISED COMPOUNDS....................................................................... 173 7.6 FINAL REMARKS ............................................................................................................................................. 174 CHAPTER 8 ................................................................................................................................................... 175 EXPERIMENTAL PROCEDURES ...................................................................................................................... 175 8.1GENERAL INFORMATION .................................................................................................................................. 175 8.1.1 Solvents and reagents ....................................................................................................................... 175 8.1.2 Analysis of data ................................................................................................................................. 175 8.1.3. Nomenclature and compound numbering ....................................................................................... 175 8.2 SYNTHETIC METHODS: CHAPTER 2 .................................................................................................................... 176 8.2.1 General method for the synthesis of 2-((dimethylamino) methylene))- cyclohexane-1,3-dione derivatives (2.3a-b) .................................................................................................................................... 176 8.2.1.1 2-((Dimethylamino)methylene)-5,5-dimethylcyclohexane-1,3-dione (2.3a) .................................. 176 8.2.1.2 2-((Dimethylamino) methylene)- cyclohexane-1,3-dione (2.3b) .................................................... 176 8.2.2 General method for the synthesis of methyl 7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline- 3-carboxylate derivatives (2.5a-b) ............................................................................................................. 177 8.2.2.1 Methyl 7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxylate (2.5a) .................. 177 8.2.2.2 Methyl 2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxylate (2.5b) ....................................... 177 8.2.3 General method for the synthesis of 2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxylic acid derivatives (2.6a-b) .................................................................................................................................... 178 8.2.3.1 7,7-Dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxylic acid (2.6a) ......................... 178 8.2.3.2 2,5-Dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxylic acid (2.6b) .............................................. 178 8.2.4 General method for the synthesis of 7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3- carboxamide derivatives using CDI as a coupling reagent (2.8a-m, 2.11a-d). .......................................... 179 8.2.4.1 N-(4-chlorophenyl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8a) ................................................................................................................................................................... 179 8.2.4.2 N-(4-bromophenyl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8b) ................................................................................................................................................................... 180 8.2.4.3 7,7-Dimethyl-2,5-dioxo-N-(p-tolyl)-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8c) .......... 180 8.2.4.4 N-(2,4-Dimethylphenyl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8d) .......................................................................................................................................................... 181 8.2.4.5 N-(2-Hydroxyphenyl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8e) ................................................................................................................................................................... 182 8.2.4.6 N-(2,4-Dimethoxyphenyl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.12f) ........................................................................................................................................................ 182 xiii 8.2.4.7 7,7-Dimethyl-2,5-dioxo-N-phenyl-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8g) ............ 183 8.2.4.8 N-(4-Chlorophenyl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8h).................. 184 8.2.4.9 N-(4-Bromophenyl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8i) .................. 184 8.2.4.10 2,5-Dioxo-N-(p-tolyl)-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8j) .............................. 185 8.2.4.11 N-(2-Hydroxyphenyl)-2,5-dioxo-1,2,5,6,7,8 hexahydroquinoline-3-carboxamide (2.8k) ............. 185 8.2.4.12 N-(2,4-Dimethoxyphenyl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8l) ....... 186 8.2.4.13 2,5-Dioxo-N-phenyl-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.8m) .............................. 187 8.2.4.14 N-(4-(4-Fluorophenyl)thiazol-2-yl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8 hexahydroquinoline-3- carboxamide (2.11a) .................................................................................................................................. 187 8.2.4.15 N-(4-(4-Methoxyphenyl)thiazol-2-yl)-7,7-dimethyl-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3- carboxamide (2.11b) .................................................................................................................................. 188 8.2.4.16 N-(4-(4-Fluorophenyl)thiazol-2-yl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.11c) ........................................................................................................................................................ 189 8.2.4.17 N-(4-(4-Methoxyphenyl)thiazol-2-yl)-2,5-dioxo-1,2,5,6,7,8-hexahydroquinoline-3-carboxamide (2.11d) ........................................................................................................................................................ 189 8.2.5 Virtual screening data ....................................................................................................................... 190 8.3 SYNTHETIC METHODS: CHAPTER 3 .................................................................................................................... 193 8.3.1 General procedure for the preparation of 3.5a and 3.5b ................................................................. 193 8.3.1.1 (E)-Methyl 2-(2-amino-4-oxothiazol-5(4H)-ylidene)acetate (3.5a) ................................................ 193 8.3.1.2 (E)-Ethyl 2-(2-amino-4-oxothiazol-5(4H)-ylidene)acetate (3.6b) ................................................... 193 8.3.1.3 Preparation of pyrrolidine-2,5-diimine (3.8) .................................................................................. 194 8.3.1.4. Preparation of 1H-1,2,4-triazol-5-amine (3.11) ............................................................................ 194 8.3.1.5 Preparation of 1H-1,2,4-triazole-5-thiol (3.13) .............................................................................. 195 8.3.1.6 Preparation of thiazol-2-amine (3.15) ........................................................................................... 195 8.3.1.7 Preparation of 2-Imino-1,3-oxazolidine 3.18 ................................................................................. 196 8.3.2 General procedures for the synthesis of 3.20a-h, 3.21a-b, 3.22a-b, 3.23a-b and 3.24. ................... 196 8.3.2.1 (E)-Dimethyl 7-(tert-butylamino)-2-(2-methoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H- thiazolo[3,2-a]pyrimidine-5,6-dicarboxylate (3.20a) ................................................................................. 197 8.3.2.2. (E)-Diethyl 7-(tert-butylamino)-2-(2-methoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H-thiazolo[3,2- a]pyrimidine-5,6-dicarboxylate (3.20b) ..................................................................................................... 197 8.3.2.3 (E)-Dimethyl 7-(tert-butylamino)-2-(2-ethoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H-thiazolo[3,2- a]pyrimidine-5,6-dicarboxylate (3.20c) ...................................................................................................... 198 8.3.2.4 (E)-Diethyl 7-(tert-butylamino)-2-(2-ethoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H-thiazolo[3,2- a]pyrimidine-5,6-dicarboxylate (3.20d) ..................................................................................................... 199 8.3.2.5 (E)-Dimethyl 7-(cyclohexylamino)-2-(2-methoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H- thiazolo[3,2-a]pyrimidine-5,6-dicarboxylate (3.20e) ................................................................................. 199 8.3.2.6 (E)-Diethyl 7-(cyclohexylamino)-2-(2-methoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H-thiazolo[3,2- a]pyrimidine-5,6-dicarboxylate (3.20f) ...................................................................................................... 200 8.3.2.7 (E)-Dimethyl 7-(cyclohexylamino)-2-(2-ethoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H-thiazolo[3,2- a]pyrimidine-5,6-dicarboxylate (3.20g) ..................................................................................................... 201 8.3.2.8 (E)-Diethyl 7-(cyclohexylamino)-2-(2-ethoxy-2-oxoethylidene)-3-oxo-3,5-dihydro-2H-thiazolo[3,2- a]pyrimidine-5,6-dicarboxylate (3.20h) ..................................................................................................... 202 8.3.2.9 Dimethyl 2-(tert-butylamino)-6-oxo-4,6,7,8-tetrahydropyrrolo[1,2-a]pyrimidine-3,4-dicarboxylate (3.21a) ........................................................................................................................................................ 202 8.3.2.10 Diethyl 2-(tert-butylamino)-6-oxo-4,6,7,8-tetrahydropyrrolo[1,2-a]pyrimidine-3,4-dicarboxylate (3.21b) ........................................................................................................................................................ 203 8.3.2.11 Dimethyl 5-(tert-butylamino)-6,7-dihydro-[1,2,4]triazolo[1,5-a]pyrimidine-6,7-dicarboxylate (3.22a) ........................................................................................................................................................ 204 8.3.2.12 Dimethyl 5-(tert-butylamino)-7H-[1,2,4]triazolo[5,1-b][1,3]thiazine-6,7-dicarboxylate ( 3.23a) 204 8.3.2.13 Methyl 5-oxo-5,8-dihydro-[1,2,4]triazolo[4,3-a]pyrimidine-7-carboxylate (3.22b) ..................... 205 8.3.2.14 Methyl 7-oxo-7H-[1,2,4]triazolo[5,1-b][1,3]thiazine-5-carboxylate (3.23b) ................................ 205 8.3.2.15 Dimethyl 7-(tert-butylamino)-5H-thiazolo[3,2-a]pyrimidine-5,6-dicarboxylate (3.24) ................ 206 xiv 8.4 SYNTHETIC METHODS: CHAPTER 4 .................................................................................................................... 207 8.4.1 General method for the synthesis of 2-amino-4H-1,3-thiazin-4-one derivatives (4.3a-e) ................ 207 8.4.1.1 2-Amino-4H-1,3-thiazin-4-one (4.3a) ............................................................................................. 208 8.4.1.2 cis,cis-, cis,trans-, trans,trans-dimethyl 3,3’-thiodiacrylate 4.3f .................................................... 208 8.4.1.3 2-Amino-6-methyl-4H-1,3-thiazin-4-one (4.3b) ............................................................................. 208 8.4.1.4 2-Amino-6-ethyl-4H-1,3-thiazin-4-one (4.3c) ................................................................................. 208 8.4.1.5 2-Amino-6-propyl-4H-1,3-thiazin-4-one (4.3d) .............................................................................. 209 8.4.1.6 2-Amino-6-phenyl-4H-1,3-thiazin-4-one (4.3e) .............................................................................. 209 8.4.2 General synthesis of 4-Oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7-dicarboxylate derivatives (4.8a-u) ...................................................................................................................................................... 209 8.4.2.1 Dimethyl 8-(tert-butylamino)-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7-dicarboxylate (4.8a) .......................................................................................................................................................... 210 8.4.2.2 Diethyl 8-(tert-butylamino)-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7-dicarboxylate (4.8b) ................................................................................................................................................................... 211 8.4.2.3 Dimethyl 8-(tert-butylamino)-2-methyl-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8c) ................................................................................................................................... 211 8.4.2.4 Diethyl 8-(tert-butylamino)-2-methyl-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8d) ................................................................................................................................... 212 8.4.2.5 Dimethyl 2-methyl-4-oxo-8-((2,4,4-trimethylpentan-2-yl)amino)-4,6-dihydropyrimido [2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8e) .................................................................................................... 213 8.4.2.6 Diethyl 2-methyl-4-oxo-8-((2,4,4-trimethylpentan-2-yl)amino)-4,6-dihydropyrimido[2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8f) ..................................................................................................... 213 8.4.2.7 Dimethyl8-(cyclohexylamino)-2-methyl-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8g) ................................................................................................................................... 214 8.4.2.8 Diethyl 8-(cyclohexylamino)-2-methyl-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8h) ................................................................................................................................... 215 8.4.2.9 Dimethyl 8-(tert-butylamino)-2-ethyl-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8i) .................................................................................................................................... 216 8.4.2.10 Diethyl 8-(tert-butylamino)-2-ethyl-4-oxo-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8j) .................................................................................................................................... 216 8.4.2.11 Dimethyl 8-((2,4-dimethylpentan-2-yl)amino)-2-ethyl-4-oxo-4,6-dihydropyrimido[2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8k) .................................................................................................... 217 8.4.2.12 Diethyl 8-((2,4-dimethylpentan-2-yl)amino)-2-ethyl-4-oxo-4,6-dihydropyrimido[2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8l) ..................................................................................................... 218 8.4.2.13 Dimethyl 8-(tert-butylamino)-4-oxo-2-propyl-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8m) .................................................................................................................................. 218 8.4.2.14 Diethyl 8-(tert-butylamino)-4-oxo-2-propyl-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8n) ................................................................................................................................... 219 8.4.2.15 Dimethyl 4-oxo-2-propyl-8-((2,4,4-trimethylpentan-2-yl)amino)-4,6-dihydropyrimido [2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8o) .................................................................................................... 220 8.4.2.16 Diethyl 4-oxo-2-propyl-8-((2,4,4-trimethylpentan-2-yl)amino)-4,6-dihydropyrimido[2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8p) .................................................................................................... 221 8.4.2.17 Dimethyl 8-(tert-butylamino)-4-oxo-2-phenyl-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8q) ................................................................................................................................... 221 8.4.2.18 Diethyl 8-(tert-butylamino)-4-oxo-2-phenyl-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8r) .................................................................................................................................... 222 8.4.2.19 Dimethyl 4-oxo-2-phenyl-8-((2,4,4-trimethylpentan-2-yl)amino)-4,6-dihydropyrimido[2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8s) ..................................................................................................... 223 8.4.2.20 Diethyl 4-oxo-2-phenyl-8-((2,4,4-trimethylpentan-2-yl)amino)-4,6-dihydropyrimido[2,1- b][1,3]thiazine-6,7-dicarboxylate (4.8t) ..................................................................................................... 224 8.4.2.21 Dimethyl 8-(cyclohexylamino)-4-oxo-2-phenyl-4,6-dihydropyrimido[2,1-b][1,3]thiazine-6,7- dicarboxylate (4.8u) ................................................................................................................................... 224 xv 8.5 SYNTHETIC METHODS: CHAPTER 5 .................................................................................................................... 226 8.5.1 Preparation of 2-Amino thiazole derivatives (5.5a-c) ....................................................................... 226 8.5.1.1 4-Methylthiazol-2-amine (5.7b) ..................................................................................................... 226 8.5.1.2.3 4,5-Dimethylthiazol-2-amine (5.7c) ............................................................................................ 226 8.5.2 Preparation of 4-phenylthiazol-2-amines derivatives (5.7d-h) ......................................................... 227 8.5.2.1 4 4-Phenylthiazol-2-amine (5.7d) ................................................................................................... 227 8.5.2.2 4-(4-Methylphenyl)thiazol-2-amine (5.7e) ..................................................................................... 227 8.5.2.3 4-(4-Fluorophenyl)thiazol-2-amine (5.7f) ....................................................................................... 227 8.5.2.4 4-(4-Chlorophenyl)thiazol-2-amine (5.7h) ..................................................................................... 228 8.5.2.5 4-(4-Methoxyphenyl)thiazol-2-amine (5.7g) .................................................................................. 228 8.5.3a Synthesis of methyl 7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate derivatives (5.17a-n). Method B (3-CR) ......................................................................................................................................... 228 8.5.3.1 Methyl 7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17a) ............................................... 229 8.5.3.2 Methyl 3-methyl-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17b) ............................... 229 8.5.3.3 Methyl 2,3-dimethyl-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17c) .......................... 230 8.5.3.4 Methyl 7-oxo-3-phenyl-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17d) ................................ 230 8.5.3.5 Methyl 7-oxo-3-(p-tolyl)-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17e) .............................. 231 8.5.3.6 Methyl 3-(4-fluorophenyl)-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17f) ................. 231 8.5.3.7 Methyl 3-(4-chlorophenyl)-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17g) ................ 232 8.5.3.8 Ethyl 7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17h) .................................................. 232 8.5.3.9 Ethyl 3-methyl-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17i) .................................... 233 8.5.3.10 Ethyl 2,3-dimethyl-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17j) ............................ 233 8.5.3.11 Ethyl 7-oxo-3-phenyl-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17k) ................................. 234 8.5.3.1 2 Ethyl 7-oxo-3-(p-tolyl)-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17l) ............................... 234 8.5.3.13 Ethyl 3-(4-fluorophenyl)-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17m) ................. 235 8.5.3.14 Ethyl 3-(4-chlorophenyl)-7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17n) ................. 236 8.5.4 Synthesis of Methyl 7-oxo-7H-thiazolo[3,2-a]pyrimidine-5-carboxylate derivatives (5.5.1a-b, 5.6a-b, 5.17a-o and 5.18a-b) Method A (2-CR)...................................................................................................... 236 8.5.4.1 N-(tert-butyl)- 7-oxo-5H-thiazolo[3,2-a]pyrimidine-5-carboxylate (5.17o).................................... 237 8.5.4.2 Methyl 5-oxo-1,5-dihydro-[1,2,4]triazolo[4,3-a]pyrimidine-7-carboxylate (5.5a) ......................... 237 8.5.4.3 Ethyl 5-oxo-5,8-dihydro-[1,2,4]triazolo[4,3-a]pyrimidine-7-carboxylate (5.5b) ............................ 238 8.5.4.4 Methyl 5-oxo-5H-[1,2,4]triazolo[3,4-b][1,3]thiazine-7-carboxylate (5.6a) .................................... 238 8.5.4.5 7-Oxo-7H-[1,2,4]triazolo[5,1-b][1,3]thiazine-5-carboxylate (5.6b) ................................................ 239 8.5.4.6 Methyl 5-oxo-3,5-dihydro-2H-oxazolo[3,2-a]pyrimidine-7-carboxylate (5.18a) ............................ 239 8.5.4.7 Ethyl 5-oxo-3,5-dihydro-2H-oxazolo[3,2-a]pyrimidine-7-carboxylate (5.18b) ............................... 240 8.6 SYNTHETIC METHODS: CHAPTER 6 .................................................................................................................... 241 8.6.1 General procedure for the synthesis of 1H-Benzo[d]imidazol-2(3H)-one derivatives (6.3a-k).......... 241 8.6.1.1 1H-Benzo[d]imidazol-2(3H)-one (6.3a) .......................................................................................... 241 8.6.1.2 Methyl-1H-benzo[d]imidazol-2(3H)-one (6.3b) .............................................................................. 242 8.6.1.3 Methyl 2-oxo-2,3-dihydro-1H-benzo[d]imidazole-5-carboylate (6.3c) .......................................... 242 8.6.1.4 5-Fluoro-1H-benzo[d]imidazol-2(3H)-one (6.3d)............................................................................ 242 8.6.1.5 5-Chloro-1H-benzo[d]imidazol-2(3H)-one (6.3e) ........................................................................... 242 8.6.1.6 5-Bromo-1H-benzo[d]imidazol-2(3H)-one (6.3f) ............................................................................ 243 8.6.1.7 1H-Benzo[d]imidazole-2(3H)-thione (6.3g) .................................................................................... 243 8.6.1.8 1H-Benzo[d]imidazol-2(3H)-imine (6.3h) ....................................................................................... 243 8.6.1.9 Methyl 2-thioxo-2,3-dihydro-1H-benzo[d]imidazole-5-carboxylate (6.3i) ..................................... 244 8.6.1.10 5,6-Dimethyl-1H-benzo[d]imidazol-2(3H)-one (6.3j) ................................................................... 244 8.6.1.11 5,6-Dichloro-1H-benzo[d]imidazol-2(3H)-one (6.3k).................................................................... 244 8.6.2 General procedure for the synthesis of 2-methyl-N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4- methanobenzo[b][1,4]diazepin-10-ylidene)propan-2-amine derivatives (6.8a-h) .................................... 244 8.6.2.1 2-Methyl-N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)propan-2-amine (6.8a) .................................................................................................................. 245 xvi 8.6.2.2 2,4,4-Trimethyl-N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)pentan-2-amine (6.8b) .................................................................................................................. 245 8.6.2.3 N-(2,2,4-Trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)cyclohexanamine (6.8c) ................................................................................................................. 246 8.6.2.4 1-Tosyl-N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)methanamine (6.8d) ...................................................................................................................... 247 8.6.2.5 2-Methyl-N-(2,2,4,7,8-pentamethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)propan-2-amine (6.8e) .................................................................................................................. 247 8.6.2.6 2,4,4-trimethyl-N-(2,2,4,7,8-pentamethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin- 10-ylidene)pentan-2-amine (6.8f) .............................................................................................................. 248 8.6.2.7 2-Methyl-N-(2,2,4,8-tetramethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)propan-2-amine (6.8g) or 2-methyl-N-(2,2,4,7-tetramethyl-2,3,4,5-tetrahydro-1,4- methanobenzo[b][1,4]diazepin-10-ylidene)propan-2-amine..................................................................... 249 8.6.2.8 N-(8-Fluoro-2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10-ylidene)-2- methylpropan-2-amine (6.8h) or N-(7-Fluoro-2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4- methanobenzo[b][1,4]diazepin-10-ylidene)-2-methylpropan-2-amine ..................................................... 249 8.6.3 General method for the synthesis of N-,3,3-Dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2- methylpropan-2-amine derivatives (6.14a-i) ............................................................................................. 250 8.6.3.1 (E)-Methyl 2-(tert-butylimino)-3,3-dimethyl-1,2,3,4-tetrahydroquinoxaline-6-carboxylate (6.14a) or (E)-methyl 3-(tert-butylimino)-2,2-dimethyl-1,2,3,4-tetrahydroquinoxaline-6-carboxylate .................. 250 8.6.3.2 (E)-methyl 3,3-Dimethyl-2-((2,4,4-trimethylpentan-2-yl)imino)-1,2,3,4-tetrahydroquinoxaline-6- carboxylate (6.14b) or (E)-methyl 2,2-dimethyl-3-((2,4,4-trimethylpentan-2-yl)imino)-1,2,3,4- tetrahydroquinoxaline-6-carboxylate ........................................................................................................ 251 8.6.3.3 (E)-N-(6-Fluoro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2,4,4-trimethylpentan-2-amine (6.14c) and (E)-N-(7-fluoro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2,4,4-trimethylpentan-2- amine (6.14d) ............................................................................................................................................. 252 8.6.3.4 (E)-N-(6-Chloro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2,4,4-trimethylpentan-2-amine (6.14e) or (E)-N-(7-chloro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2,4,4-trimethylpentan-2- amine ......................................................................................................................................................... 253 8.6.3.5 (E)-N-(6,7-Dichloro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2-methylpropan-2-amine (6.14f) ........................................................................................................................................................ 253 8.6.3.6 (E)-N-(6,7-Dichloro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2,4,4-trimethylpentan-2- amine (6.14g) ............................................................................................................................................. 254 8.6.3.7 (E)-N-(3,3-Diethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2-methylpropan-2-amine (6.14h) ......... 254 8.6.3.8 (E)-N-(6,7-Dichloro-3,3-diethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2-methylpropan-2-amine (6.14i) ......................................................................................................................................................... 255 8.6.4 General procedure for the synthesis of 2-methyl-N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4- methanobenzo[b][1,4]diazepin-10-ylidene)propan-2-amine derivatives using Acetone-d6 (6.8i-l) (Green- deuterated-atoms) ..................................................................................................................................... 256 8.6.4.1 2,4,4-Trimethyl-N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)pentan-2-amine (6.8i -D) ............................................................................................................... 256 8.6.4.2 N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)cyclohexanamine (6.8j D) .............................................................................................................. 257 8.6.4.3 2-Methyl-N-(2,2,4,7,8-pentamethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10- ylidene)propan-2-amine (6.8k D) ............................................................................................................... 257 8.6.4.4 2,4,4-Trimethyl-N-(2,2,4,7,8-pentamethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin- 10-ylidene)pentan-2-amine (6.8l D) ........................................................................................................... 258 8.6.5 General method for the synthesis of N-,3,3-Dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2- methylpropan-2-amine derivatives using Acetone-d6 (6.14h-j) ................................................................. 258 8.6.5.1 (E)-N-(3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2-methylpropan-2-amine (6.14h D) ... 259 8.6.5.2 (E)-N-(6,7-Dichloro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2-methylpropan-2-amine (6.14i D) ..................................................................................................................................................... 259 xvii 8.6.5.3 (E)-N-(6,7-Dichloro-3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2,4,4-trimethylpentan-2- amine (6.14j-D) .......................................................................................................................................... 260 8.6.6 General method for the synthesis of 2,2,4-Trimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepine derivatives (6.12a-b) .................................................................................................................................. 260 8.6.6.1 2,2,4,7,8-Pentamethyl-2,3-dihydro-1H-benzo[b][1,4]diazepine (6.12a) ........................................ 261 8.6.6.2 7,8-Dichloro-2,2,4-trimethyl-2,3-dihydro-1H-benzo[b][1,4]diazepine (6.12b) ............................... 261 8.6.7 General procedure for the synthesis of 6.13a-b ................................................................................ 262 8.6.7.1 7.8-Dimethyl-N-(tert-butyl)-2,4,4-trimethyl-2,3,4,5-tetrahydro-1H-benzo[b][1,4]diazepine-2- carboxamide (6.13a) .................................................................................................................................. 262 8.6.7.2 7,8-dichloro-N-cyclohexyl-2,4,4-trimethyl-2,3,4,5-tetrahydro-1H-benzo[b][1,4]diazepine-2- carboxamide (6.13b) .................................................................................................................................. 263 8.6.8 General method for the synthesis of 4-oxo-4,5-dihydro-benzodiazepine-2-carboxylates (6.16a-j) .. 263 8.6.8.1 Methyl 4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16a) ............................... 264 8.6.8.2 Ethyl 4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16b) .................................. 264 8.6.8.3 Tert-butyl 4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16c) ........................... 265 8.6.8.5 Ethyl 7-nitro-4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16e) or ethyl 8-nitro-4- oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate ....................................................................... 266 8.6.8.6 Tert-butyl 7-nitro-4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16f) or tert-butyl 8-nitro-4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate ....................................................... 267 8.6.8.7 Methyl 7,8-dichloro-4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16g) .......... 267 8.6.8.8 Ethyl 7,8-dichloro-4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16h) .............. 268 8.6.8.9 Tert-butyl 7,8-dichloro-4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16i) ....... 268 8.6.8.10 Methyl 7,8-dimethyl-4-oxo-4,5-dihydro-1H-benzo[b][1,4]diazepine-2-carboxylate (6.16j) ........ 269 8.7. X-RAY CRYSTALLOGRAPHY .............................................................................................................................. 269 Table 8.7.1(Chapter 3) Crystal data and structure refinement for 3.20a, 3.20e, 2.21a, 3.22a and 2.23b 270 Table 8.7.2 (Chapter5) Crystal data and structure refinement for 5.17b, 5.17c, 5.17e, 5.17g and 5.6a ... 270 Table 8.7.3 (Chapter 6)Crystal data and structure refinement for 5.8a, 5.8k, 5.14f and 5.14g ................ 271 8.8 PRELIMINARY MOLECULAR MODELING ............................................................................................................... 273 8.8.1 Ligand preparation ............................................................................................................................ 273 8.8.2 The absorption, distribution, metabolism and excretion (ADME) properties ................................... 273 8.8.3 Preparation of HIV IN-1 protein ........................................................................................................ 273 8.8.4 Molecular docking of synthesised compounds into HIV IN binding site ............................................ 273 8.9 BIOLOGICAL EVALUATION METHODS .................................................................................................................. 274 8.9.1 Development of a LEDGF/p75-HIV-1 IN AlphaScreen assay .............................................................. 274 8.9.2 Development of a Dimerization AlphaScreen Assay ......................................................................... 275 8.9.3 Alphascreen assays ........................................................................................................................... 275 8.9.3.1 LEDGF/p75-HIV-1 IN assay ............................................................................................................. 275 8.9.3.2 Multimerization assay .................................................................................................................... 276 8.9.4 Cytotoxicity assay .............................................................................................................................. 276 8.9.5 Antimicrobial assay ........................................................................................................................... 277 8.9.6 Antiviral assay ................................................................................................................................... 279 REFERENCES ................................................................................................................................................. 280 APPENDIX, PRESENTATION OF SELECTED DATA .......................................................................... 292 CHAPTER 2: SELECTED SPECTROSCOPIC DATA ......................................................................................... 292 CHAPTER 3: SELECTED SPECTROSCOPIC DATA ......................................................................................... 300 CHAPTER 4: SELECTED SPECTROSCOPIC DATA ......................................................................................... 312 CHAPTER 5: SELECTED SPECTROSCOPIC DATA ......................................................................................... 322 CHAPTER 6: SELECTED SPECTROSCOPIC DATA ......................................................................................... 335 xviii 2-Methyl-N-(2,2,4-trimethyl-2,3,4,5-tetrahydro-1,4-methanobenzo[b][1,4]diazepin-10-ylidene)propan-2- amine derivatives 6.8 ................................................................................................................................. 335 (E)-N-(3,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-ylidene)-2-methylpropan-2-amine derivatives 6.14 .. 342 Diazepine -based acetone-d6 (6.8) ............................................................................................................. 349 Quinoxaline-based (6.14) acetone-d6 page ................................................................................................ 352 Diazepines 6.13 and 6.16 ........................................................................................................................... 357 CHAPTER 1 Literature review 1.1 Introduction to multicomponent reactions Multicomponent reactions (MCRs) are also known as one-pot reactions that comprise of at least three reactants chosen to form a single product containing building blocks of atoms from all the reactants.1,2,3 The general practical concept of MCRs is depicted in Figure 1.1 adopted from Rocha and co-workers,4 which shows at least four different reactants with different functional groups converging to form one product. Figure 1.1: Schematic representation of multicomponent reactions (Rocha and co-workers4) There are a number of well-known MRCs such as a) the Ugi four-component reaction5 (U- 4CR), b) the Passerini three-component reaction6, 7 (P-3CR), c) the Biginelli three-component reaction8 (B-3CR) and d) the Hantzsch three-component reaction9 (H-3CR) represented in Figure 1.2. MCRs have been exploited for over 100 years; the initial discovery and report of an MCR remains difficult to identify, however, the Strecker10 multicomponent reaction (S-3CR) was reported in 1850 followed by the Hantzsch dihydropyridine (DHP) synthesis in 1882. The Biginelli 3-CR was reported in 1891 while the Mannich11 reaction (M-CR) was reported in 2 1912. The first isocyanide-based MCRs (IMCR) was reported in 1921 and 1959 by Passerini6 (3-CR) and Ugi,12 respectively. N CR1R3 O H2N R2HO R4 O N R2 R3 O NH R4 O R1 Ugi 4-CR R2 O O O R3 H2N NH2 X R1 H O X: O,S,NH N H NH R1 XR2 O O R3 Biginelli 3-CR R2 OH O N CR1R3 R4 O O N H R1 R2 O O R4R3 Passerini 3-CR R2 O O O R3 R4 H O R1 NH2 N R4 R1 R2 CO2R3R3O2C R2 Hantzsch 3-CR a b c d Figure 1.2: Examples of MRCs: a) Ugi, b) Passerini, c) Biginelli and d) Hantzsch. MCRs are considered a convenient approach in synthetic chemistry and have many advantages over the traditional one or two component reactions by reducing the number of sequential multiple reactions required and often producing better yields.13,14 The most famous MCRs are the Passerini and Ugi reactions which regained attention in the early 1990s.15,16 These reactions rely on the dual electrophilic/nucleophilic reactivity of the isocyanide carbon to provide distinct complex products. The reactions of isocyanides in MCRs are well represented by the Passerini 3-CR, Ugi 3-CR and Ugi 4-CR.17,18 MCRs continue to attract attention in medicinal chemistry and drug discovery applications, due to the possibility of readily obtaining different heterocyclic frameworks of interest.19 Interestingly, MCRs additionally possess considerable potential for contributing to green 3 production processes and protocols of pharmaceuticals, by generating complex products in a single step.20,21 Compared to sequential multistep reactions, MCRs contribute significantly to minimising the large amount of waste generated daily in pharmaceutical and industrial production.20,22,23, ,24 The following sections summarise the history and use of MCRs, the elegant chemistry that they offer, the use of this approach in drug discovery, and the considerable use of MCRs in “green” chemical production and production of natural products. 1.2. Strecker reaction (S-3CR) The Strecker reaction10 was first reported in 1850 after condensation of an aldehyde 1.1 with a cyanide source 1.2 in the presence of ammonia 1.3 to gave intermediate 1.4 followed by hydrolysis of the nitrile group to form an amino acid 1.5 as shown in Scheme 1.1. R1 O NH3HCN N H H HR1 CN N H H HR1 CO2H Aqueous media Hydrolysis 1.4 1.5 1.1 1.2 1.3 Scheme 1.1: The Strecker 3-CR (S-3CR) The fact that the Strecker reaction occurs in aqueous medium and under catalyst-free conditions makes it one of the favourable methods for application in industries and laboratories because it is a convenient approach to produce amino acids, natural products and bioactive compounds. Another factor to consider is the commercial availability and affordability of the substrates required. 25,26,27 To date the Strecker reaction has produced a myriad of publications and is still under ongoing investigation. There are several biologically active compounds produced using the S-3CR, such as boron-containing retinoids,28 hepatitis C virus NS3 serine protease inhibitors29 and (±)-phthalascidin 622.30 Several methods used for the synthesis of amino acids and bioactive compounds involve the use of catalysts, such as Al-MCM-41,31 nanocrystalline magnesium oxide,32 BINOL-phosphoric acid,33 N-heterocyclic carbene (NHC)-amidate palladium(II) complex,34 gallium (III) triflate35 and bisformamides.36 However, the use of catalysts and non-green solvents results in additional work-up steps and the requirement for 4 additional waste treatments. Based on these disadvantages there is a continuous search for safer and more practical Strecker methods to synthesise bioactive compounds. 1.3. Hantzsch reaction (H-3CR) The first Hantzsch 3-CR was reported in 1882 after an aldehyde 1.6 and two equivalents of a β-ketoester 1.7 were condensed in the presence of a nitrogen donor 1.8 to give dihydropyridine (DHP) derivatives 1.9 9, 37,38 as shown in Scheme 1.2. R2 O O O R3 R4 H O R1 NH2 N R4 R1 R2 CO2R3R3O2C R2 H2O Reflux 1.9 1.6 1.7 1.8 Scheme 1.2: The Hantzsch 3-CR (H-3CR) Dihydropyridines are considered a significant group of heterocyclic compounds in drug discovery and they can also be found in nature.39,40,41 There are several catalysts which have also been comprehensively applied to promote the formation of the DPH ring such as ferric chloride (Fe3Cl) or potassium permanganate, nano-γ-Fe2O3-SO3H,42 Al-MCM-41 and Fe/Al- MCM-41,43 CuBr2, 44 SiO2/P2O5-SeO2, 45 H2O2/Co(OAc)2 46 and Na2S2O4/TBHP.47 In consideration of green chemistry principles48 and the use of safe practices in laboratories, functionalised Brønsted acidic ionic liquids are used to replace traditional catalysts used for synthesis of DPH derivatives: Sharma and co-workers49 used a SO3H-functionalised imidazolium ionic liquid, Liu and co-workers50 used 3-(N,N-dimethyldodecylammonium) propanesulfonic acid hydrogen sulphate ([DDPA][HSO4]), Hu and co-workers51 used H2O2 catalysed by V2O5 in ionic liquid [C12mim][HSO4], and Lui and Lui52 used 3-(N,N- dimethyldodecylammonium) propanesulfonic acid hydrogen sulphate ([DDPA][HSO4]) with NaNO3. The formation of the DPH ring as represented in Scheme 1.3 (see Katritzky and co- workers)53 occurs by reaction of an aldehyde with a β-ketoester to give one intermediate 1.10, and the nitrogen source reacts with another molecule of β-ketoester to form another intermediate 1.11. These two intermediates subsequently react to generate intermediate 1.12, leading to the formation of DPH 1.9. 5 R2 O O O R2 O HN O R3 R1 R4 N R4 R1 R2 CO2R3R3O2C R2 O H N R4 R1 R2 CO2R3R3O2C R2 HO N R4 R1 R2 CO2R3R3O2C R2 1.10 1.12 1.13 1.9 R3 1.11 Scheme 1.3: Formation of DPH via H-3CR 1.4. Biginelli reaction (B-3CR) The 3-CR Biginelli reaction8 was discovered in 1891 and involves condensation of an aldehyde 1.14 with a β-ketoester 1.7 in the presence of urea 1.15 or thiourea or guanidine hydrochloride under acidic catalysis to obtain 3,4-dihydropyrimidin-2(1H)-one (DHMP) 1.16 as shown in Scheme 1.4 R2 O O O R3 H2N NH2 X R1 H O X: O,S,NH N H NH R1 XR2 O O R3 Biginelli 3-CR 1.16 1.14 1.7 1.15 Scheme 1.4: The Biginelli 3-CR (B-3CR) The B-3CR initially had some challenges with poor yields and a very small substrate scope range. The discovery of the first B-3CR was followed by a thorough investigation into understanding the course of the reaction and structural variations. The reactions towards the formation of DHMP were explored by investigating solvent compatibility and effects, acid catalyst and increasing substrate scope.54 The exploration was extended from solution reactions 6 to solid phase reactions using microwave assistance. The DHMPs have interesting biological activities such as calcium channel modulation,55 antimicrobial and antitubercular activity.56 The proposed mechanism of the B-3CR (see Kappe)57 is shown in Scheme 1.5. A Lewis or a Brønsted acid activates the aldehyde at event 1 in order to react with urea/thiourea to form a hemiaminal species which leads to the elimination of water forming an N-acyliminium cation at event 2. The carbocation at event 2 readily reacts with the nucleophilic α-carbon atom centre of a β-ketoester to form an open chain ureide at intermediate 3, followed by ring closing to form a hexahydropyrimidine intermediate and elimination of water to form DHMP. There are other alternative mechanisms reported and discussed in the literature.58,59 O R4 O O H2N NH X R1 H O H R2 R1 N H NH X R2 H O N H R1 NHR2 X O O N N H R1 O O X R2 R4 OH N N H R1 O O X R2 R4 H2O 1.16 3 carbocation open chain ureide hexahydropyrimidine H=acid X= O, S, NH R3, R4= alkyl, aryl R3 R3 R3R3 H 1 2 Scheme 1.5: Possible mechanism for the Biginelli 3-CR (B-3CR). 1.5. Passerini reaction (P-3CR) Isocyanide-based multicomponent reactions (IMCRs) have gained much prestige, interest and growth over the last few decades. This area has become one of the exciting and robust tools for peptidomimetic synthesis. The first IMCR was reported by Passerini6 as a 3-CR in 1921 after the reaction of a carboxylic acid 1.17 with an aldehyde or ketone 1.18 in the presence of an isocyanide 1.19 to give rise to an α-acyloxy carboxamide product 1.20 containing both amide and ester functionalities as shown in Scheme 1.6. 7 R2 OH O N CR1R3 H O O N H R1 R2 O O R4R3 Passerini 3-CR 1.20 1.17 1.18 1.19 Scheme 1.6: The Passerini 3-CR (P-3CR) The first proposal by Passerini was that the reaction mehanism might involve a zwitterion intermediate. The extensive research described in the literature to investigate the Passerini reaction mechanism has suggested various intermediates including carbocations, hemiacetals and hydrogen-bonded adducts.60 However, the original Passerni reaction mechanism is generally considered to be a concerted reaction, especially in apolar solvents as shown in Scheme 1.7.61 The reaction proceed by the activation of an aldehyde by the carboxylic acid and subsequent addition of an isocyanide to form nitrilium as shown at events 1 and 2. The nitrilium is trapped by the carboxylate followed by a Mumm rearrangement leading to the α-acyloxy amide 1.20 O H O OR2 H R3 C N R1 O OR2 R3O H H N R1 O N H R1 R2 O O R3 1 2 1.20 Scheme 1.7: Nucleophilic and electrophilic reactivity of the isocyanide carbon is illustrated for the Passerini reaction. Maeda and co-workers61 used the artificial force induced reaction (AFIR) method in gas phase for studdying the Passerini reaction mechanism. In their study it shows that the mechanism may involve an extra acidic component prior to the desired product, which shows the Passerini reaction as a pseudo four-component reaction shown in Scheme 1.8. 8 R1 OH O N CR4 R2 R3 O R2 R3 O O O R1 H R2 R3 O O O R1 H NR4 OR1 O N R2 OH R3 R4 R1 OH O O R1 O N R2 O R3R4 H O O R1H R1COOH O O R1 HO R3 R2 N R4 R1 OH O O O R1 O R3 R2 N R4 R1 O O H H R1COOH R1 O O O R3 R2 H N R4 Scheme 1.8: Passerini reaction mechanism using AFIR method in gas phase (pseudo-four component reaction) The mechanism proposed by Maeda and co-workers was supported by the studies done by Ramozzi and Morokuma62 and also Alvim and co-workers58 after perfoming high-level DFT calculations which also show a pseudo four-component reaction (Scheme 1.9). These studies also reveal that the nitrilium intermediate (B) is stable in solution and its generation is a rate- determing step, catalysed by an extra carboxylic acid molecule leading to Mumm rearrangement and affording 1.20 as the final product. 9 R1 OH O R2 H O OO R1 H OR1 O H O R2 H NC R3 OO R1 H OR1 O H O R2 C N R3 H B nitrilium O R2O HH N R3 R1 O R1 O O H C imidate Mumm reaarangement O O O R1 H N R3 H R2 R1 O OH OR1 O R2 H N H O R3 R1COOH 1.20 Scheme 1.9: Passerini reaction mechanism using high-level DFT in solution (pseudo-four component reaction) 1.5.1 Substrate scope in the Passerini reactions The scope of the Passerini reaction has been widely studied and some of the reaction components can be replaced by suitable isosteres. The first acid isostere used by Ugi63 was hydrazoic acid (HN3) 1.21 and aluminium azide Al(N3)3 1.23 in the Passerini reaction, which was regarded as a template for the synthesis of α-hydroxy tetrazoles 1.25 (Scheme 1.10). Alternatively NaN3 1.22 can also be used in place of HN3 1.21. 10 R1 R2 O N CR3 HN3 Al(N3)3 N N N NR2 OH R1 R3 1.241.19 1.21 1.23 1.25 or 1.22 NaN3 Scheme 1.10: Passerini reaction for synthesis of hydroxy tetrazoles. Zahoor and co-workers64 prepared peptidomimetic compounds 1.29 by reacting protected γ- oxo-amino acids 1.26, carboxylic acid 1.27 and isocyanide 1.28 as a neat reaction (Scheme 1.11). O N H F3C COOt-Bu O R OH O N C 1.26 1.27 1.28 N H COOMe O AcO R t-BuOOC neat 1.29 MeOOC HN CF3 O Scheme 1.11: Passerini reaction for preparation of peptidomimetic compounds. Recyclable magnetic core-shell nanoparticle supported TEMPO (2,2,6,6-tetramethyl- piperidin-1-oxyl) catalyst was applied for the oxidative synthesis of Passerini products 1.34, by reacting caboxylic acid 1.30, isocyanide 1.31 and primary or secondary alcohol 1.32 using toluene as a solvent at room temperature (Scheme 1.12).65 Presumably, in situ oxidation of the alcohol is followed by the 3-CR Passerini reaction. R2 OH O N CR3 1.30 1.31 R1 OH TEMPO Toluene R3 O O N R1 OH R2 R2 O O R1 HN O R3 1.32 1.33 1.34 Mumm rearangement Scheme 1.12: Passerini reaction using TEMPO catalyst. 11 Basso and co-workers66 reacted carboxylic acid 1.30, isocyanide 1.31, and diazoketones 1.35 under photocatalytic conditions to produce 3-CR product 1.36. Under these conditions, the ketenes generated in situ from 1.35, are able to participate in the three-component reaction (Scheme 1.13). Piperylene Heptane1.35 R1 O N2 N H R3 O OO R2 R1 1.36 R2 OH O N CR3 1.30 1.31 Scheme 1.13: Passerini reaction for synthesis of ketenes. Neo and co-workers67 reacted isocyanide 1.31, carboxylic acid 1.37 and α-keto-aldehyde 1.38 to give product 1.39. The desired β-keto-amides 1.40 were achieved via metal-mediated removal of the acetoxy group (Scheme 1.14). OH O N CR1 1.37 1.31 1.38 Ar O O H Ar N H R O O O O Ar N H R1 OO Zn, NH4Cl 1.39 1.40MeOH Scheme 1.14: Passerini reaction for synthesis of β-keto-amides 1.5.2 Chirality in Passerini reactions The strategies and methods for controlling the stereochemical outcome of carbon-carbon bond forming reactions from the achiral substrates used in Passerini reaction are finite. The generation of a highly enatioselective Passerini 3-CR is one of the most significant goals. 12 Kusebauch and co-workers68 used stoichiometric amounts of a Ti-taddol complex 1.43 as a catalyst to obtain moderate enantioselectivity of α-acyloxyamides with 32–42% ee as shown in Scheme 1.15. R1 H O N CR2 1.41 1.31 1.42 R3 O OH O O H Ph Ph Ph OH Ph Ti(i-OPr)4 R3 O O R1 H N O R2 32- 42% ee 1.43 1.44 Scheme 1.15: Enantioselective Passerini reaction using Ti-taddol complex Zhu and co-workers69 obtained moderate to excellent yield of α-acyloxyamides enantioselectively using stable aluminium salen complex 1.45 as a chiral Lewis acid catalyst from isocyanides 1.31, non chelating aldehydes 1.41 and carboxylic acids 1.42 (Scheme 1.16). N N t-Bu t-Bu t-But-Bu OO Al Cl Toluene R2 O O R1 H N O Ar1.45 1.46 52-68% 68->99% ee R1 H O N CR2 1.41 1.31 1.42 R3 O OH Scheme 1.16: Passerini enantioselective reaction using aluminium salen complex 13 Andreana and co-workers70 managed to achieve good yields of product 1.48 with reasonable enantioselectivity using isocyanide 1.31, chelating aldehydes 1.41 and carboxylic acid 1.42 after employing chiral tridentate Lewis acidic Cu-pybox complex 1.47 as a catalyst (Scheme 1.17). 62- 98% ee N O N N O Cu DCM 2 OTf 2 R3 O R1 H N O R2 75- 75% 1.47 1.48 R1 H O N CR2 1.41 1.31 1.42 R3 O OH Scheme 1.17: Enantioselective Passerini reaction using Cu-pybox complex Zhang and co-workers71 activated the reaction of isocyanide 1.31, aldehyde 1.41, and carboxylic acid 1.42 using chiral phosphoric acid 1.49 to obtain high yields of enantioselective products 1.50 (Scheme 1.18) O O P O HO R3 O R1 H N O R2 1.49 DCM 1.50 up to 99% up to 99% ee R1 H O N CR2 1.41 1.31 1.42 R3 O OH Scheme 1.18: Passerini enantioselective reaction using chiral phosphoric acid. 14 1.6. Ugi reaction: U-4CR and U-3CR 1.6.1 Ugi-four component reaction (U-4CR) The definitive Ugi reaction is a four-component reaction (U-4CR) between an isocyanide 1.51, amine 1.52, carbonyl compound 1.53 (aldehyde or ketone) and carboxylic acid 1.54 to give product 1.55 (Scheme 1.19).5 N CR1 R3 O H2N R2 HO R4 O N R2 R3 O NH R4 O R1 Ugi 4-CR 1.55 1.54 1.52 1.531.51 Scheme 1.19: The Ugi 4-CR (U-4CR) During the Ugi-4CR a carbonyl compound 1.53 reacts with an amine 1.52 to form an imine intermediate at event 1. The imine is activated by the carboxylic acid proton and it is then attacked by the isocyanide leading to the nitrilium intermediate which is then attacked by the conjugate base of the carboxylic acid at event 2. This is followed by the Mumm rearangement at event 3 to give the final product 1.26 (Scheme 1.20).14,72 15 NHR3 R2 C N R1 R3 NH R2 N R1 O R4 O HN R2 R3 O N R1 R4 O H N R2 R3 O NH R4 O R1 1.55 1 2 3 R3 O H2N R2 1.521.53 Mumm rearangement Scheme1.20: Nucleophilic and electrophilic reactivity of the isocyanide carbon is illustrated for the Ugi reaction. The use of the Ugi reaction for the synthesis of a tripeptide from the reaction of amino acid 1.56, dimethoxybenzylamine 1.57, chiral isocyanide 1.58 and aldehyde 1.59 was reported by Mroczkiewicz and Ostaszewski.73 The peptide aldehyde 1.61 was achieved after deprotection and oxidation of 1.60 (Scheme 1.21). 16 N H OH O Cbz NH2 O O O N OAc N H Cbz N O Dmb N H O OAc N H Cbz H N O N H O O 1.56 1.57 1.58 1.59 1.60 1.61 C Scheme 1.21: Synthesis of a tripeptide using U-4CR. Che and co-workers74 describe the use of coumarin-3-carboxylic acid 1.62, isocyanide 1.63, aniline 1.64 and pyridine-2-aldehyde 1.65 in U-4CR to achieve annulated products 1.67. The intramolecular annulation depends on the nature of the aldehyde in application: only pyridine- 2- and pyridine-4-aldehydes gave rise to the annulated product, whereas the conventional U- 4CR product 1.66 was obtained when benzaldehyde or pyridine-3-aldehydes were emplyoyed (Scheme 1.22). 17 O O OH O N C NH2 N O H O O N O OH HN O O N OH N HN O H 1.62 1.63 1.64 1.65 1.66 1.67 Scheme1.22: Synthesis of Ugi adducts The reaction of a secondary amine 1.68, glycolaldehyde dimer 1.69, isocyanide 1.70 and carboxylic acid 1.71 gave rise to a novel MCR scaffold 1.73.75 This reaction proceeded differently from classical U-4CR intermediate 1.72, because the secondary amine prevents the usual Mumm rearangement from occuring and the hydroxyl group from the glycolaldehyde permits O-acyl rearangement to occur, leading to a novel scaffold (Scheme 1.23). R H N R O O OH HO R2 OH O R1 N C N N O R2 O R R R1 OH N H N O R R R1 OR2 O 1.68 1.69 1.70 1.71 1.72 1.73 Scheme 1.23: Ugi reaction using glycolaldehyde dimer 18 1.6.2 Ugi-three component reaction (U-3CR) The U-3CR was initialy described in 1960 while investigating water as a nucleophile.76 The reaction involved isocyanide 1.51, primary amine 1.52 and an aldehyde 1.53 in the presence of water and a catalyst (Scheme 1.24). However, there are many Ugi-3CRs reported under different conditions to the one mentioned here (Scheme 1.24). N CR1 Ugi 3-CR 1.51 HN N R2 R1 H O R3 R3 O H2N R2 1.52 1.53 1.74 H2OH Catalyst Scheme 1.24: The Ugi 3-CR The mechanism is quite similar to U-4CR, however carboxylate in this case is replaced by a molecule of water that attacks the electrophilic carbon that might be activated by the catalyst, which consequently in many cases eliminates the Mumm rearangement (Scheme 1.25).72 NHR3 R2 C N R1 R3 NH R2 N R1 HN R2 R3 O N R11 3 R3 O H2N R2 1.521.53 H O H H H HN N R2 R1 H O R3 Catalyst 1.74 Scheme 1.25: Ugi 3-CR mechanism 19 Ramezanpour and co-workers77 used the U-3CR for synthesis of hydrazino amides 1.78 from the reaction of isocyanides 1.51, cyclohexanone 1.76 and hydrazides 1.77 and using ethanol as a solvent (Scheme 1.26). There were several catalysts that were employed and tested for this reaction such as p-toluenesulfonic acid (p-TsOH), ZnCl2 and ZrOCl2, S-1,1-binaphthyl-2,2- diylhydrogen phosphate, phosphorous acid (H3PO4) and camphor sulfonic acid. O R1 R2 N H O NH2 N CR3 R2 N H H N O N R1 O R3 H 1.76 1.77 1.51 1.78 Catalyst EtOH Scheme 1.26: Ugi-3CR for synthesis of hydrazino amides. Shaabani and co-workers78 describe the ability of zinc chloride to act as a catalyst for the Ugi- 3CR of cyclohexyl isocyanide 1.79, 2-aminophenols 1.80 and aldehydes 1.81 using methanol as a solvent at room temperature to achieve synthesis of N-cyclohexyl-2-(2- hydroxyphenylamino)acetamides 1.82 (Scheme 1.27). R1 NH2 OH R2 R3 H O N C H N N H OOH R2 R3 R1 ZnCl2 1.80 1.81 1.79 1.82 MeOH Scheme 1.27: Ugi-3CR for synthesis of N-cyclohexyl-2-(2-hydroxyphenylamino)acetamides Faggi and co-workers79 reported the reaction of isocyanide 1.51, aniline 1.83 and 2- formylbenzoic acid 1.84 to afford isocoumarins 1.86 (Scheme 1.28). Hoever in this case one of the reagents, formylbenzoic acid 1.84, contains two components of carboxylic acid and an aldehyde that participate in the product formation. These types of reactions are regarded as 4 centre Ugi 3CR. interestingly, they where able to obtain the product prior to Mumm rearangement after optimising conditions and applying low nucleophilicity amines. The reactions were carried out at higher temperatures or in the presence of trace acid to afford Ugi adducts. 20 H O OH O Ar NH2 N CR O NH H N O R Ar N CONHR O Ar H 1.84 1.83 1.51 1.85 1.86 MeOH Scheme 1.28:4 Centre-Ugi-3CR for synthesis of isocoumarins. These types of reactions are dominated by formation of a new stereogenic centre and the products are reported as racemic. The challenges related to enantioselective U-3CR, U-4CR and Passerini reactions include: spontaneous background reaction in appropriate solvent at room temperatures, product inhibition causes low catalyst turnover, complexity of the possible mechanism pathways and the possibility of the isocyanide coordinating to the metal catalyst. 1.7. van Leusen reaction (V-3CR) The van Leusen 3-CR involves reaction of α-substituted tosylmethyl isocyanide (TosMIC) 1.87, a primary amine 1.88 and an aldehyde 1.89 to give rise to imidazole 1.90.80,81 The reaction occurs in the presence of solvents such as methanol, dimethoxyethane or water with base including potassium carbonate or sodium hydride as shown in Scheme 1.29. NTs R3 R1 NH2 R2 H O N N R2 R1 R3 1.90 1.87 1.891.88 Solvent Base C Scheme 1.29: van Leusen 3-CR The 3-CR van Leusen reaction generally proceeds by the initial reaction of the primary amine 1.88 with an aldehyde to form a Schiff base which reacts with deprotonated TosMIC at event 1 in order to react with activated TosMIC to give the intermediate shown at event 2. Here an internal nucleophililic attack occurs leading to cyclisation to form intermediate 3 followed by elimination of p-toluenesulfinic acid to afford imidazole 1.90 (Scheme 1.30).82 21 R1 NH2 OR2 N R2 R1 NTs R3 NTs R3 base N N Ts R2 R3 H R1 N N Ts R2 R3 R1 base-TsH N N R2 R1 R3 1.87 1 341.90 1.88 1.89 C C NR2 Ts N R3 R1 C 2 Scheme 1.30: van Leusen 3-CR mechanism 1.8 The application of dimethyl acetylenedicarboxylate in organic synthesis Dimethyl acetylenedicarboxylate (DMAD) is an electron deficient alkyne diester which exists as a liquid at room temperature and is highly electrophilic. DMAD versatility makes it useful in cycloaddition reactions as a dienophile and a dipolarophile. In addition, DMAD is also used to form carbon-carbon bonds and in multicomponent reactions for developing heterocyclic scaffolds.83 In line with the essential discovery of DMAD reactions with heterocyclic compounds by Diels and co-workers84 and Acheson and Elmore,85 the utility of DMAD in organic synthesis has gained tremendous attention.86,87 The common fundamental properties and applications of DMAD in organic synthesis includes Michael reactions, Diels-Alder, 1,3- dipolar and [2+2] cycloadditions and in MCRs. DMAD is one of the economically affordable and accessible reagents. The preparation of DMAD was originally reported by Bandrowski88 in 1877, after brominating maleic acid 1.91 to form intermediate 1.92 which is dehydrohalogenated by potassium hydroxide resulting in 1.93 which was treated with excess sulfuric acid to yield compound 1.94. Compound 1.94 was then esterified with methanol and sulfuric acid to afford DMAD 1.95 (Scheme 1.31). 22 OHO OH O Br2,H2O OHO OH O Br Br KOH CO2KKO2C CO2HHO2C H2SO4 (excess) MeOH H2SO4CO2MeMeO2C 1.91 1.92 1.93 1.941.95 Scheme 1.31: Preparation of DMAD. 1.8.1 DMAD and isocyanides in multicomponent reactions Isocyanide-based multicomponent reactions (IMCRs) are considered as one of the special subclasses in chemical synthesis, which are extremely versatile and interesting. IMCRs possess considerable potential that lies in the diversity of bond-formations and high substrate scope. This subclass comprises of interesting chemistry, which includes a nucleophile and an electrophile reacting at the same atom, leading to formation of adducts. The reaction of isocyanides with DMAD was first described by Winterfeldt and co-workers89 as an exceptional reaction that required more attention. The addition of neutral nucleophiles to electrophilic acceptors generates a transient zwitterion intermediate. One of the known examples of DMAD in MCRs, arises from the reaction of an isocyanide with DMAD (event 1, Scheme 1.32) leading to a zwitterion adduct (event 2) which might be trapped in different ways to give multiple reaction possibilities.15 One possibility is that the zwitterion reacts with a nucleophile possessing an acidic proton. Under these conditions, the two possible pathways for the zwitterion (event 2) to react are shown in Scheme 1.32. The first step that occurs is deprotonation of the nucleophile containing an acidic proton such as C-H, N-H, O-H or SH. Subsequently, the anionic nucleophile may possibly attack the nitrilium ion via a 1,2 route (path A) or a 1,4 route (path B) to yield an imine 1.95 or ketenimine 1.96, respectively, as shown in Scheme 1.31. 23 CO2MeMeO2C N CR CO2Me C MeO2C N R 1 2 CO2Me C MeO2C N R CO2Me C MeO2C N R Nu-H Nu-H CO2Me C MeO2C N R CO2Me C MeO2C N R Nu H H Nu NuH 3 4 1.96 1.95 H Nu path A path B Scheme 1.32: Possible zwitterion reaction pathways with nucleophile. The second possible reaction of a zwitterion generated from an isocyanide and DMAD involves an electrophile. During this development event the electrophile 1.97 acts as a dipolarophile, where the zwitterion at event 1 initially attack the electrophilic centre giving rise to a nucleophile which subsequently attacks the nitrilium ion. One of the examples reported by Shabaani and co-workers90 is represented in Scheme 1.33. MeO2C C CO2Me N R O O O CO2MeMeO2C C O O O N R CO2MeMeO2C N O O R 1.97 1.98 1.991 Scheme 1.33: Zwitterion reaction with an electrophile. 24 1.8.1.1 Synthesis of heterocyclic scaffolds using zwitterions and nucleophiles containing acidic protons. Shaabani and co-workers91 reported the synthesis of chromene derivatives using a zwitterion adduct formed by isocyanides and DMAD to react with 2,5-dihydroxycyclohexa-2,5-diene- 1,4-dione 1.100 containing an acid proton (C-H) as shown in Scheme 1.34. The proposed mechanism proceeds by the removal of a proton from compound 1.100 at event 1 followed by 1,4-nucleophilic attack by a carbon nucleophile at event 2 to give the ketenimine. The intramolecular attack by oxygen on the ketenimine at event 3 leads to the formation of chromene 1.101, in instances where there is excess isocyanide and DMAD the same reaction proceeds on the second hydroxyl group to afford compound 1.102. O O O O MeO2C HN R MeO2C NH R CO2Me CO2Me CO2Me C MeO2C N R 1 O O OH O O O OH O MeO2C HN R MeO2C 1.100 1.101 H CO2Me C MeO2C N R 2 O O OH O 1.102 O O OH O MeO2C MeO2C C NR H 3 Scheme 1.34: Synthesis of chromene derivatives 25 Shaabani and co-workers92 reported the one-pot three-component reaction of alkyl isocyanide 1.51 with DMAD 1.95 in the presence of triphenylphosphonium bromide 1.103 which contains an acidic C-H using dichloromethane as a solvent at room temperature. The resulting six- membered heterocyclic compounds 1.104 were obtained in a yield range of 51% - 63% as shown in Scheme 1.35. N CR DMAD 1.51 1.95 DCM O Ph3P O Br N CO2Me CO2Me O Ph3P O R 1.103 1.104 Scheme 1.35: Synthesis of 6-membered heterocyclic compounds from triphenylphosphonium bromide. The reaction of isocyanide 1.51 with DMAD 1.95 in the presence of compound 1.105 consisting of an acidic proton (C-H) using acetonitrile as a solvent at room temperature gave rise to pyrano[2,3-c]pyrazole derivatives93 (Scheme 1.36). N N H O Ph N CR DMAD 1.51 1.95 MeCN N N O Ph CO2Me CO2Me HN R 1.105 1.106 Scheme 1.36: Synthesis of pyrano[2,3-c]pyrazole derivatives Zangouei and co-workers94 reported a facile one-pot synthesis method using isocyanide 1.51, DMAD 1.95 and 2,3-dihydro-5H-[1,3]thiazolo[3,2-a]pyrimidine-5,7(6H)-dione 1.107 which contains an acidic C-H to afford pyranothiazolopyrimidines 1.108 using N,N- dimethylformamide as solvent at 100 °C (Scheme 1.37). N CR DMAD 1.51 1.95 N NS O O DMF N NS O O H N CO2Me CO2Me R 1.107 1.108 26 Scheme 1.37: Synthesis pyranothiazolopyrimidine derivatives. Esmaeili and co-workers95 reported the reaction of isocyanide 1.51 and DMAD 1.95 with 2- imino-1,3-thiazolidin-4-one 1.109 containing an acidic N-H proton and the internal nucleophile to react with the ketenimine as shown at event 3, to afford 3-oxo-2,3-dihydro-5H- [1,3]thiazolo[3,2-a]pyrimidines 1.110 (Scheme 1.38). CO2Me C MeO2C N R 1 CO2Me C MeO2C N R 2 MeO2C MeO2C C NR SN O NH H SN O NH 1.109 N NS O CO2Me CO2Me NH R 1.110 S N O HN 3 Scheme 1.38: 3-oxo-2,3-dihydro-5H-[1,3]thiazolo[3,2-a]pyrimidine derivatives. Hassanabadi and co-workers96 reported the reaction of isocyanide 1.51 and DMAD 1.95 in the presence of benzimidazole carbamate 1.111 which contains an acidic proton (N-H) and internal nucleophile to afford 2H-pyrimido[1,2-a]benzimidazoles 1.112 (Scheme 1.39) N H N NH O O N CR DMAD 1.51 1.95 N N N O O NH CO2Me CO2Me R DCM 1.111 1.112 Scheme 1.39: Synthesis of 2H-pyrimido[1,2-a]benzimidazoles derivative. 27 Ghandi and co-workers97 reported the reaction of 3-acetyl-2Hchromen-2-ones 1.113 with a zwitterion adduct to obtain cyclopentadiene-fused chromanones 1.114 in moderate to good yield under reflux using toluene as solvent (Scheme 1.40). O O O CO2MeMeO2C N CMe3 O O O MeO2C CO2Me N CMe3 O O MeO2C CO2Me CO2Me NH CMe3 1 2 1.113 O O O MeO2C CO2Me N CMe3 3 1.114 Scheme 1.40: Synthesis of cyclopentadiene-fused chromanones derivative. 1.8.1.2 Synthesis of heterocyclic scaffods using zwitterions and electrophiles The reaction of isocyanide 1.51 and DMAD 1.95 with phthalic anhydride 1.115 at room temperature using dichloromethane as a solvent gave rise to benzo-fused spirolactones 1.116 as shown in Scheme 1.41. 90 O O O N CR DMAD 1.51 1.95 O O O N CO2Me CO2Me 1.115 1.116 R DCM Scheme 1.41: Synthesis of benzo-fused spirolactones derivatives. 28 Zhao and co-workers98 reported the reaction of two molecules of isocyanide 1.51 and DMAD 1.95 in the presence of carbon dioxide to afford dioxospiro compounds 1.118 using toluene as a solvent at 80 ºC (Scheme