4 Bioactive pyridines in microbiology 3 studies

patology for microbiology

1. Bioactive Pyridines H H N nicotine N H N N S N H 2 O O sulphapyridine • Nicotine is pharmacologically active constituent of tobacco - toxic and addictive • Sulphapyridine is a sulfonamide anti-bacterial agent - one of the oldest antibiotics N H 2 O N H Me N N Me N paraquat isoniazide • Paraquat is one of the oldest herbicides - toxic and non-selective • Isoniazide has been an important agent to treat tuberculosis - still used, but resistance is a significant and growing problem 16

2. Drugs Containing a Pyridine Me O O N N O O Me S N H N Name: Nexium Company: AstraZeneca Disease: Acid reflux S N O N H O Name: Actos_Pioglitazone Company: Eli Lilly N O O O Me S N H N Name: Aciphex-Rabeprazole Company: Eisai Disease: Duodenal ulcers and acid reflux H N N N H N N N O Name: Gleevec-Imatinib Company: Novartis Disease: Type 2 diabetes 17 Disease: Chronic myeloid leukemia

3. Pyridines - Structure 1.40 Å 1.39 Å 2.2 D 1.17 D N 1.34 Å N N H • Isoelectronic with and analogous to benzene • Stable, not easily oxidised at C , undergoes substitution rather than addition • −I Effect (inductive electron withdrawal) • −M Effect δ + δ + δ + N N N N N δ− • Weakly basic - pK a ~5.2 in H 2 O (lone pair is not in aromatic sextet) • Pyridinium salts are also aromatic - ring carbons are more δ+ than in parent pyridine etc. N H N N H H 18

4. Pyridines - Synthesis The Hantzsch synthesis (“5+1”) O Me Me Me Ph H O O O O Ph Me N O O Me NH 3 pH 8.5 Me Me aldol condensation Me and dehydration O O Me HNO 3 Me Me oxidation Me Ph O Me Me O O Me Michael addition H Ph O Me Me N Me H O H Ph O Me Me OO Me O H Ph O Me Me O H 2 N Me • The reaction is useful for the synthesis of symmetrical pyridines • The 1,5-diketone intermediate can be isolated in certain circumstances • A separate oxidation reaction is required to aromatise the dihydropyridine 19

5. Pyridines - Synthesis From Enamines or Enamine Equivalents - the Guareschi synthesis (“3+3”) C O 2 Et C N Me N O H C N H 2 N O K 2 CO 3 Me C O 2 Et O H 2 N O C N Me K 2 CO 3 Et O 2 C Me C N N Me 73% • The β-cyano amide can exist in the ‘enol’ form Using Cycloaddition Reactions (“4+2”) Me Me C O 2 H O N Diels-Alder cycloaddition C O 2 H Me Me H + O Me N Me C O 2 H H H O Me − H 2 O Me Me N Me 70% C O 2 H H H H O N C O 2 H N • Oxazoles are sufficiently low in aromatic character to react in the Diels-Alder reaction 20

6. Pyridines - Electrophilic Reactions Pathways for the Electrophilic Aromatic Substitution of Pyridines γ β E α N E E N E E N − E E N E • The position of the equilibrium between the pyridine and pyridinium salt depends on the substitution pattern and nature of the substituents, but usually favours the salt 21

7. Pyridines - Electrophilic Reactions Regiochemical Outcome of Electrophilic Substitution of Pyridines β N α N E H γ N E H E H N N E H N E H E H N N E H N E H E H • Resonance forms with a positive charge on N (i.e. 6 electrons) are very unfavourable • The β-substituted intermediate, and the transition state leading to this product, have more stable resonance forms than the intermediates/transition states leading to the 22 • γ products

8. Pyridines - Electrophilic Reactions Regiochemical Outcome of Electrophilic Substitution of Pyridinium Ions β N E α N E E H γ N E E H E H N E N E E H N E E H E H N E N E E H N E E H E δ + H δ + δ + N • Regiochemical control is even more pronounced in the case of pyridinium ions • In both pyridine and pyridinium systems, β substitution is favoured but the reaction is slower than that of benzene 23 • Reaction will usually proceed through the small amount of the free pyridine available

9. Pyridines - Electrophilic Reactions N Substitution N B F 4 N O 2 O C Substitution NO 2 BF 4 O R Cl N Cl R MeI N N Me SO 3 , CH 2 Cl 2 N S O 3 • Reaction at C is usually difficult and slow, requiring forcing conditions • Friedel-Crafts reactions are not usually possible on free pyridines 24

10. Pyridines - Electrophilic Reactions Nitration of Pyridine N O 2 c-H 2 SO 4 , c-HNO 3 300 °C, 24 h N N 6% ! Use of Activating Groups Me Me Me N O 2 c-HNO 3 , oleum 100 °C Me N Me Me N Me Me N Me H 90% Me Me Me N O 2 MeI c-HNO 3 , oleum 100 °C Me N Me Me N Me Me N Me I Me I Me 70% • Multiple electron-donating groups accelerate the reaction • Both reactions proceed at similar rates which indicates that the protonation at N occurs 25 prior to nitration in the first case

11. Pyridines - Electrophilic Reactions Sulfonation of Pyridine S O 3 H H 2 SO 4 , SO 3 (low yield) N HgSO 4 , H 2 SO 4 , 220 °C N Hg S O 3 N 70% • Low yield from direct nitration but good yield via a mercury intermediate Halogenation of Pyridine Cl Br Cl 2 , AlCl 3 , Br 2 , oleum 100 °C 130 °C N N N 33% 86% • Forcing reaction conditions are required for direct halogenation 26

12. Pyridines - Reduction Full or Partial Reduction of Pyridines R R R H 2 , Pt, Na - NH 3 , AcOH, rt EtOH N N N H H Na, EtOH R N H • Pyridines generally resist oxidation at ring carbon atoms and will often undergo side-chain oxidation in preference to oxidation of the ring • Full or partial reduction of the ring is usually easier than in the case of benzene 27

13. Pyridines - Nucleophilic Reactions Regiochemical Outcome of Nucleophilic Addition to Pyridines α N Nu Nu β N Nu γ N H Nu H Nu Nu N N H N H Nu H Nu Nu N N H N H Nu H Nu Nu N N H N • Nitrogen acts as an electron sink • β Substitution is less favoured because there are no stable resonance forms with the negative charge on N • Aromaticity will is regained by loss of hydride or a leaving group, or by oxidation 28

14. Pyridines - Nucleophilic Reactions Nucleophilic Substitution X Nu Nu N N X X = Cl , Br , I , ( N O 2 ) Nu = Me O , N H 3 , Ph S H etc. • Favoured by electron-withdrawing substituents that are also good leaving groups • The position of the leaving group influences reaction rate (γ > α >> β) Cl N O 2 Relative rate 80 Cl NaOEt N Cl N 40 O Et N Cl N Cl N 1 3 × 10 −4 29

15. Pyridinium Ions - Nucleophilic Reactions Nucleophilic Substitution X Nu Nu N N X R X = Cl , Br , I , ( N O 2 ) R Nu = Me O , N H 3 , Ph S H etc. • Conversion of a pyridine into the pyridinium salt greatly accelerates substitution • Substituent effects remain the same (α, γ >> β) but now α > γ Cl O 2 N O O N O 2 N N Me Me Cl Cl Cl N Cl N N N Me Me Me 30 Relative rate 5 × 10 7 1.5 × 10 4 1 10 −4

16. Pyridines - Pyridyne Formation Substitution via an Intermediate Pyridyne H N H 2 benzyne Cl Cl NaNH 2 N H N H 2 N NaNH 2 N H N H 2 H 2 N N H 2 N N 27% H 2 N H N H 2 N H 2 N N 44% • When very basic nucleophiles are used, a pyridyne intermediate intervenes • Pyridynes are similar to benzynes and are very reactive (not isolable) 31

17. Pyridines - Nucleophilic Reactions Nucleophilic Attack with Transfer of Hydride PhLi, Et 2 O, 0 °C Ph N LiNH 2 − H 2 H 2 N H O 2 (air) N Ph N Li H 2 O LiNH H N H Li 2 2 N N H N N Li H N HX X = H ( N H 3 ) / 2-aminopyridine • A hydride acceptor or oxidising agent is required to regenerate aromaticity • The reaction with LiNH 2 is referred to as the Chichibabin reaction 32

18. Pyridines - Metal-Halogen Exchange Direct Exchange of Metal and a Halogen X N n -BuLi X = Cl , Br , I Li n -Bu X N • Halogenated pyridines do not tend to undergo nucleophilic displacement with alkyl lithium or alkyl magnesium reagents • Metallated pyridines behave like conventional Grignard reagents N Li Br Li n -BuLi, PhC N Ph Et 2 O, − 78 °C N N N O N H Ph H 2 O Ph N N 33

19. Pyridines - Directed Metallation Use of Directing Groups Me O Me O O Me Li I O O O t -BuLi, I(CH 2 ) 2 Cl Et 2 O, − 78 °C N N N 90% O Ph O Li O O Me N i -Pr 2 N i -Pr 2 N i -Pr 2 Me LiTMP, − 78 °C O N N N Ph N Me 2 • Directing groups allow direct lithiation at an adjacent position N Li LiTMP Me Me • A Lewis basic group is required to complex the Lewis acidic metal of the base 34

20. Oxy-Pyridines - Structure Oxy-Pyridines/Pyridones α N O H N O N O H H zwitterion O H O O 1,3-dipole O γ N N N N H H H zwitterion O H O O O O β N N N N N H H H H zwitterion • Subject to tautomerism • The α, γ systems differ from the β systems in terms of reactivity and structure • In the α case, the equilibrium is highly solvent dependent, but the keto form is favoured in polar solvents 35

21. Amino Pyridines - Structure Amino Pyridine Systems etc. N N H N N H 2 N N H 2 H • Contrast with oxy-pyridines • Amino pyridines are polarised in the opposite direction to oxy-pyridines 36

22. Oxy-Pyridines - Reactions Electrophilic Substitution Br O H O H Br 2 , H 2 O, rt N Br N Br O O N O 2 c-H 2 SO 4 , c-HNO 3 100 °C, 2 days N N H H 38% • Reactions such as halogenation, nitration, sulfonation etc. are possible • N is much less basic than that in a simple pyridine • Substitution occurs ortho or para to the oxygen substituent (cf. phenols) 37

23. Oxy-Pyridines - Reactions Nucleophilic Substitution PCl 5 Cl N O N O H H P Cl 3 Cl P Cl 4 Cl N Cl H Cl O P Cl 3 • Replacement of the oxygen substituent is possible Cl P Cl 3 N O Cl H Cl P Cl 3 N O Cl H • In this case, the reaction is driven by the formation of the very strong P=O bond 38

24. Oxy-Pyridines - Reactions Cycloaddition O Me O N Me Me C O 2 Me Me C O 2 Me Me N C O 2 Me C O 2 Me • Oxy-pyridines have sufficiently low aromatic character that they are able to participate as dienes in Diels-Alder reactions with highly reactive dienophiles 39

25. Alkyl Pyridines - Deprotonation Deprotonation with a Strong Base CH 3 PhLi N O R 1 R 2 CH 2 CH etc. N N O H R 1 R 2 N • Deprotonation of α and γ alkyl groups proceeds at a similar rate, but β alkyl groups are much more difficult to deprotonate • Bases are also potential nucleophiles for attack of the ring 40

26. Pyridinium Salts - Reactions Nucleophilic Attack with Reducing Agents H B H 3 NaBH 4 , EtOH N Me H B H 3 N Me N Me H 3 B H N N Me H B H 3 Me N N Me Me • Nucleophilic attack is much easier (already seen this) • Deprotonation of alkyl substituents is easier (weak bases are suitable) • Ring opening is possible by attack of hydroxide H N N O N O O 2 N O H O 2 N O H O 2 N etc. 41 N O 2 N O 2 N O 2

27. Pyridine N -Oxides N -Oxide Formation RCO 3 H N N N N O O O O Cl O O H meta -chloroperoxybenzoic acid ( m -CPBA) • The reactivity N -oxides differs considerably from that of pyridines or pyridinium salts • A variety of peracids can be used to oxidise N but m -CPBA is used most commonly • N -Oxide formation can be used to temporarily activate the pyridine ring to both nucleophilic and electrophilic attack 42

28. Pyridine N -Oxides Electrophilic Substitution H N O 2 H N O 2 N O 2 c-H 2 SO 4 , c-HNO 3 , N 100 °C N N N O O O O • The N -oxide is activated to attack by electrophiles at both the α and γ positions • Nitration of an N -oxide is easier than nitration of the parent pyridine • Reactivity is similar to that of a pyridinium salt in many cases e.g. nucleophilic attack, deprotonation of alkyl groups etc. Removal of O N O 2 N O 2 N O 2 PPh 3 N N N O O O P Ph 3 P Ph 3 P Ph 3 • Deoxgenation is driven by the formation of the very strong P=O bond 43

29. Pyridines - Synthesis of a Natural Product Synthesis of Pyridoxine (Vitamin B 6 ) Using the Guareschi Synthesis Et O O Me O H O O H H O Me N C N Et O H 2 N O piperidine, EtOH, heat Me N H 90% Et O H 2 N 1. NaNO 2 , HCl, 90 °C 2. 48% HBr (neat) 3. AgCl, H 2 O, heat Me N 40% Et O C N O 2 N c-HNO 3 , Ac 2 O, 0 °C O Me Et O N H 2 O 2 N H 2 , Pd/Pt, AcOH Me C N N O H 32% PCl 5 , POCl 3 , 150 °C C N N Cl 40% • The final sequence of steps involves formation of a bis -diazonium salt from a diamine • Pyridoxine performs a key role as the coenzyme in transaminases 44

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