Metal Species for Amide Hydrolysis. Literature Seminar, Kiyomichi SHINODA (M1)

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1 Metal Species for Amide ydrolysis Literature Seminar, Kiyomichi SIDA (M1)

2 Table of Contents 1 Introduction 2 Residue- or Sequence-Selective ydrolysis of Amides 3 Protein-Selective ydrolysis of Amides

3 1 Introduction

4 1 Introduction Characteristics of Amide Bond stability toward hydrolytic cleavage Me t 1/2 = 500 years p = 6.8, 25 C Me + 2 A. Radzicka, R. Wolfenden, J. Am. Chem. Soc. 1996, 118, This stability derives from resonance effect. R 1 R 2 resonance effect R 1 R 2 inactive toward nucleophilic attack

5 1 Introduction Characteristics of Amide Bond planar structure due to the resonance effect R 1 R 2 resonance effect R 1 R 2 R 1 R 2 twist angle distribution of tertiary amides (A. J. Kirby et al., J. Chem. Soc., Perkin Trans , 522.)

6 1 Introduction Destabilizing Amide Bond activation by Lewis acid R 1 R 2 Lewis acid δ+ R 1 LA R 2 cleavage R R 2 activation by bond distortion R 1 R 2 bond distortion R 1 δ + R2 cleavage R 1 + R 2 R 1 R 2 R 2 R 1

7 1 Introduction Precedents: Activation by Lewis Acid hydrolysis by cerium(iv)-cyclodextrin complex 2 Ph Ce( 4 ) 2 ( 3 ) 6 (1 eq.) γ-cd (5 eq.) 0.1 M Tris buffer (0.01 M) p 8.0, 60 C, 24 h Ph 39% conversion M. Komiyama et al., J. Chem. Soc., Chem. Commun. 1994, Zinc-catalyzed solvolysis Cbz Me Zn(Tf) 2 (5 mol%) diethylcarbonate (2 eq.) n-bu (2 M) reflux, 45 h Cbz 84% yield n-bu K. Mashima et al., Angew. Chem. Int. Ed. 2012, 51, 5723.

8 1 Introduction Precedents: Activation by Bond Twisting molecules containing twisted amide 2-quinoclidone 1-aza-2-adamantanone (Kirby's Amide) total synthesis of the former: K. Tani & B. M. Stoltz, ature 2006, 441, 731. (tetrafluoroborate salt) the latter: A. J. Kirby et al., J. Chem. Soc., Perkin Trans. 2, 2001, 522. characters BF 4 twist angle bond length C Å Å Å (Values are cited from the above 2 papers.)

9 1 Introduction Precedents: Activation by Bond Twisting hydrolysis of twisted amides C 2 D BF 4 t1/2 < 15 s D 2, r.t. 2 2 C over a few minutes K. Tani & B. M. Stoltz, ature 2006, 441, 731. A. J. Kirby et al., J. Am. Chem. Soc., 1998, 120, 7101.

10 1 Introduction In This Seminar... activation by Lewis acid R 1 R 2 Lewis acid δ+ R 1 LA R 2 cleavage R R 2 activation by bond distortion R 1 R 2 bond distortion R 1 δ + R2 cleavage R 1 + R 2 R 1 R 2 R 2 R 1

11 2 Residue- or Sequence-Selective ydrolysis of Amides

12 2 Residue- or Sequence-Selective ydrolysis of Amides Palladium(II) Complexes 2 2 Pd Pd Pd MeS S β-cd [Pd( 2 ) 4 ] 2+ [Pd(en)( 2 ) 2 ] 2+ β-cd =

13 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ substrate: Met-peptide Ac-Ala-Lys-Tyr-Gly-Gly-Met-Ala-Ala-Arg-Ala- hydrolysis condition Met-peptide [Pd( 2 ) 4 ] 2+ (1 eq.) aqueous media (1 mm) p 2.3, 60 C 24 h fragments. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, 4759.

14 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ experiment procedure 60 C 5 min 1 h 12 h 22 h 24 h color change PLC sample PLC sample PLC sample 5 min: [Pd(2)4] 2+ was bound to the peptide. (checked by PLC and MALDI MS) 24 h: two components were observed.. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, 4759.

15 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ PLC charts 60 C 5 min 1 h 12 h 22 h 24 h color change PLC sample PLC sample PLC sample 2 peaks were separated by PLC and MALDI mass spectroscopic identification was conducted.. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, 4759.

16 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ composition of the fractions -Gly-Met-Ala-Ala-Arg-Ala- Ac-Ala-Lys-Tyr-Gly-! Ac-Ala-Lys-Tyr-Gly-Gly-Met-Ala-Ala-Arg-Ala-. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, 4759.

17 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ TCSY 1 MR spectrum before addition of Pd complex 5 min after the addition. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, SMe singlet: 2.12 ppm 2.45 ppm Pd(II) complex was bound to the Met6 side chain.

18 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ TCSY 1 MR spectrum before addition of Pd complex 5 min after the addition. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, Met6-C signal disappeared: deprotonated complete coordination of amide to the Pd(II) ion

19 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ TCSY 1 MR spectrum before addition of Pd complex 24 h after the addition (reaction finished). M. Kostić et al., J. Am. Chem. Soc. 2002, 124, Signals derived from Gly5 and Met6 disappeared. Amide cleavage occurred at Gly4-Gly5.

20 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ equilibrium among Pd(II) complexes active inactive 2 and 3 exists at p 2.3, and 3 is major.. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, 4759.

21 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(2)4] 2+ 2 is hydrolytically active, but 3 is hydrolytically inactive. Pd S 2 2 hydrolysis + Pd S 2 Pd 2 S 3 hydrolysis coordination of 2 amide nitrogen atoms Lewis acidity of Pd(II) ion was quenched. + Pd 2 S. M. Kostić et al., J. Am. Chem. Soc. 2002, 124, 4759.

22 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(en)(2)2] 2+ substrate: oxidized chain B of bovine insulin -Phe-Val-Asn-Gln-is-Leu-Cys X -Gly-Ser-is-Leu-Val- -Glu-Ala-Leu-Tyr-Leu-Val-Cys X -Gly-Glu-Arg-Gly-Phe- -Phe-Tyr-Thr-Pro-Lys-Ala- hydrolysis condition oxidized chain B of bovine insulin [Pd(en)( 2 ) 2 ] 2+ (5 eq.) aqueous media (1 mm) p 2.0, 60 C 4 days fragments. M. Kostić et al., Inorg. Chem. 2002, 41, 7053.

23 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(en)(2)2] 2+ cleavage site!! -Phe-Val-Asn-Gln-is-Leu-Cys X -Gly-Ser-is-Leu-Val- -Glu-Ala-Leu-Tyr-Leu-Val-Cys X -Gly-Glu-Arg-Gly-Phe- -Phe-Tyr-Thr-Pro-Lys-Ala- Pd(II) reagent promoted cleavage of the second bond upstream from the is5 and is10 anchor. (characterized by MALDI mass spectroscopic identification and amino acid analysis: -terminal Edman degradation). M. Kostić et al., Inorg. Chem. 2002, 41, 7053.

24 2 Residue- or Sequence-Selective ydrolysis of Amides Acidic ydrolysis with [Pd(en)(2)2] 2+ equilibrium among Pd(II) complexes R 1 R Pd 2 R 1 R 2 2 Pd 2 [Pd(en)( 2 ) 2 ] 2+ R 1 2 and 3 exists at p 2.0 R 2 2 R 2 Pd 2 Pd 2 R active inactive R 2. M. Kostić et al., Inorg. Chem. 2002, 41, R 1 [Pd(en) 2 ] Pd

25 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with [Pd(2)4] 2+ substrates & cleavage site! GlyMet-peptide: Ac-Ala-Lys-Tyr-Gly-Gly-Met-Ala-Ala-Arg-Ala- SarMet-peptide: Ac-Lys-Gly-Gly-Ala-Gly-Sar-Met-Ala-Ala-Arg-Gly- ProMet-peptide: Ac-Lys-Gly-Gly-Ala-Gly-Pro-Met-Ala-Ala-Arg-Gly-!!. M. Kostić et al., J. Am. Chem. Soc. 2003, 125, 781.

26 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with [Pd(2)4] 2+ dependence on p of the 1st-order-rate const. reaction: peptide [Pd( 2 ) 4 ] 2+ (1 eq.) aqueous media (1 mm) 60 C fragments Why? ProMet > SarMet > GlyMet ProMet- and SarMet-peptide can be cleaved but GlyMet-peptide can t. Why?. M. Kostić et al., J. Am. Chem. Soc. 2003, 125, 781.

27 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with [Pd(2)4] 2+ difference between GlyMet- (left) and ProMet- (right) peptide in equilibrium among Pd(II) complexes R Pd 2 S active (minor*) R 2 2 Pd 2 S R 2 1 Pro 2 Pd 2 S Pd R (* at p 2.3) 4 S inactive (major*) R Pd 2 3 R S 2 Pd S 2 2 Pro active. M. Kostić et al., J. Am. Chem. Soc. 2003, 125, 781.

28 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with [Pd(2)4] 2+ TCSY 1 MR spectrum (ProMet-peptide) before addition of Pd complex signals derived from Met7 disappeared. Met7 group coordinates to Pd(II) ion 10 min after addition of 1 eq. Pd complex signals of other residues persisted. ther amide groups were not bound either.. M. Kostić et al., J. Am. Chem. Soc. 2003, 125, 781.

29 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with [Pd(2)4] 2+ external attack vs internal delivery in this case.... M. Kostić et al., J. Am. Chem. Soc. 2003, 125, 781.

30 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with [Pd(2)4] 2+ external attack vs internal delivery RESY 2 Pd S 2 Pd S 2 cis-gly-pro trans-gly-pro RESY 1 MR spectrum showed the cross peak between the Gly5α-C and Pro6δ-C external attack (trans-gly-pro). M. Kostić et al., J. Am. Chem. Soc. 2003, 125, 781.

31 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with Pd(II)-β-CD complex substrate: Met-peptide Ac-Lys-Gly-Gly-Phe-Ser-Pro-Phe-Phe-Ala-Ala-Arg-Ala- hydrolysis condition Pd 2 2 MeS S β-cd (10 eq.) peptide aqueous media (1 mm) p 7.5, 60 C 24 h fragments. M. Kostić et al., J. Am. Chem. Soc. 2004, 126, 696.

32 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with Pd(II)-β-CD complex cleavage site! Ac-Lys-Gly-Gly-Phe-Ser-Pro-Phe-Ala-Ala-Arg-Ala- Pd(II)-β-CD complex promoted cleavage of the first one upstream from the Pro6-Phe7 sequence. (characterized by MALDI mass spectroscopic identification). M. Kostić et al., J. Am. Chem. Soc. 2004, 126, 696.

33 2 Residue- or Sequence-Selective ydrolysis of Amides eutral ydrolysis with Pd(II)-β-CD complex possible interaction toward sequence selectivity CD cavities bind hydrophobic substrates in aqueous media.. M. Kostić et al., J. Am. Chem. Soc. 2004, 126, 696.

34 2 Residue- or Sequence-Selective ydrolysis of Amides Summary of This Section residue-selective hydrolysis sequence-selective hydrolysis. M. Kostić et al., J. Am. Chem. Soc. 2003, 125, M. Kostić et al., J. Am. Chem. Soc. 2004, 126, 696.

35 3 Protein-Selective ydrolysis of Amides

36 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease catalyst design catalyst site : Cyc-metal complex binding site : peptide nucleic acid (PA) J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

37 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease Based on this design, the library of Cyc-containing PA oligomers was constructed. n=7, 8: no activities* toward Mb (Cu(II)-complex) n=9: active* toward Mb (Cu(II)-complex) (* checked by SDS-PAGE) J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

38 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease their own combinatorial library Cu(II)1 was the best. J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

39 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease changing metal center from Cu(II) to Co(III) Metal transfer to metal-abstracting materials in living body should be slower for Co(III) complexes because of the exchange-inertness of Co(III) Cu(II) 2.0 μm Furthermore, Co(III)1 shows high reactivity than Cu(II)1. Co(III) 0.47 μm k0(cu) = h -1 k0(co) = h -1 (pseudo-1st-order kinetics) decrease of [Mb] (p 7.5, 37 ) J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

40 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease affinity of Co(III)1 complex to Mb Two straight lines intersect at C0 = [Mb]0 = 4.7 μm. [Mb]0 = 4.7 μm p= 7.5, 37 Km < 4.7 μm < 5.0 μm (cf. Km of fumarase = 5.0 μm) [Mb}0 Affinity of Co(III)1 complex to Mb was high enough. kcat (not kcat/km) should be considered!! J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

41 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease kcat comparison between Co(III) complexes Co(III)1 was the best! p dependence of kcat for cleavage of Mb by Co(III)1 complex most active at physiological p! J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

42 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease possible cleavage mechanism This mechanism consistents with the p dependence of Co(III)1 complex. The following two would reduce the reactivity of Co(III)1 complex. protonation of the hydroxo (T) or oxo (T ) ligand at low p deprotonation of the ammonium ion (T ) at high p r.d.s. J. Suh et al., J. Biol. Inorg. Chem. 2009, 14, 151.

43 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease cleavage site characterization -terminal sequencing (Edman degradation) was conducted to product solution of Co(III)3. Leu89-Ala90 was the cleavage site. J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

44 3 Protein-Selective ydrolysis of Amides Mb-Selective Artificial Protease selectivity (control experiment) albumin, γ-globulin, elongation factor P, gelatin A, gelatin B Above 5 proteins were incubated with Cu(II)1 or Co(III)1, but protein cleavage was not observed. Target selectivity can be expected! J. Suh et al., Bioorg. Med. Chem. 2003, 11, 2901.

45 3 Protein-Selective ydrolysis of Amides PDF-Selective Artificial Protease PDF: peptide deformylase involved in deformylation of the formyl-methionyl derivative of proteins formed in the prokaryotic translational systems. Its inhibitors are searched as candidates for new antibiotic drugs. way toward catalytic drugs J. Suh et al., J. Am. Chem. Soc. 2005, 127, 2396.

46 3 Protein-Selective ydrolysis of Amides PDF-Selective Artificial Protease construction of a library of catalyst candidates synthesized by the Ugi reaction (product was racemic mixture) R R 2 + R 3 + R 4 R 1 C R 2 R 3 R 4 analysis of the result (PDF-cleaving activity) examined by MALDI-TF mass spectrum J. Suh et al., J. Am. Chem. Soc. 2005, 127, 2396.

47 3 Protein-Selective ydrolysis of Amides PDF-Selective Artificial Protease property of screening PDF (5 µm) cat. (1.5-3 µm) overnight p 7.5, 37 C fragments examined by MALDI-TF mass spectrum the result of screening 2 most active complex: Co 2 2 J. Suh et al., J. Am. Chem. Soc. 2005, 127, 2396.

48 3 Protein-Selective ydrolysis of Amides PDF-Selective Artificial Protease cleavage site p 7.5, 37 orange: PDF / green: fragment C-terminal sequencing by carboxy peptidase A Glu152-Arg153 was the cleavage site. optimum p = 7.5 / lower limit of kcat = 0.05 h -1 J. Suh et al., J. Am. Chem. Soc. 2005, 127, 2396.

49 3 Protein-Selective ydrolysis of Amides PDF-Selective Artificial Protease docking study result S-isomer of the catalyst with PDF was more stable than with the R-isomer. Central acyclic chain of the catalyst interacted with the C-terminal α-helix, while the 3 aromatic tails made contact with the helical and the loop structures residing above the active site. J. Suh et al., J. Am. Chem. Soc. 2005, 127, 2396.

50 3 Protein-Selective ydrolysis of Amides PDF-Selective Artificial Protease selectivity (control experiment) 15 other proteins were examined, but none of them were cleaved by the Co(III) complex. list: Application to Drug is possible! 2 Co 2 2 J. Suh et al., J. Am. Chem. Soc. 2005, 127, 2396.

51 3 Protein-Selective ydrolysis of Amides AmPs-Selective Artificial Protease AmPs: amyloidgenic peptides or proteins lacking active sites Conventional approaches can t be applied. related to diseases Peptide-cleaving catalysts is suitable for their drug! target AmPs of this research amyloid β protein (Aβ): Alzheimer s Disease human islet amyloid polypeptide (h-iapp): type 2 diabetes J. Suh et al., Chem. Soc. Rev. 2008, 38, 1949.

52 3 Protein-Selective ydrolysis of Amides AmPs-Selective Artificial Protease construction of a library of catalyst candidates synthesized according to the route shown below Aromatic moieties were employed as auxiliary binding components in the combinatorial library. J. Suh et al., Angew. Chem. 2007, 119, 7194.

53 3 Protein-Selective ydrolysis of Amides AmPs-Selective Artificial Protease property of screening Aβ (4.0 µm) cat. p 7.5, 37 C 24 h fragments examined by MALDI-TF mass spectrum 4 complexes were selected. Aβ40: active Aβ42: active Aβ40: active Aβ42: active Aβ40: inactive Aβ42: active Aβ40: inactive Aβ42: active J. Suh et al., Angew. Chem. 2007, 119, 7194.

54 3 Protein-Selective ydrolysis of Amides AmPs-Selective Artificial Protease property of screening h-iapp (4.0 µm) cat. p 7.5, 37 C 24 h fragments examined by MALDI-TF mass spectrum J. Suh et al., J. Biol. Inorg. Chem. 2008, 13, 693.

55 3 Protein-Selective ydrolysis of Amides AmPs-Selective Artificial Protease 8 complexes were selected. Aβ40: active Aβ42: active h-iapp: active Aβ40: active Aβ42: active h-iapp: active Aβ40: inactive Aβ42: active h-iapp: active Aβ40: inactive Aβ42: active h-iapp: active Aβ40: inactive Aβ42: inactive h-iapp: active Aβ40: inactive Aβ42: inactive h-iapp: active Aβ40: inactive Aβ42: inactive h-iapp: active Aβ40: inactive Aβ42: inactive h-iapp: active J. Suh et al., J. Biol. Inorg. Chem. 2008, 13, 693.

56 3 Protein-Selective ydrolysis of Amides AmPs-Selective Artificial Protease selectivity (control experiment) horse heart myoglobin, bovine serum γ-globulin, bovine serum albumin, human serum albumin, chicken egg white lysozyme, chicken egg ovalbumin, bovine pancreas insulin Above 7 proteins were incubated with from A to, but protein cleavage was not observed. Application to Drug is possible! (Drug for all AmPs may be possible...?) J. Suh et al., J. Biol. Inorg. Chem. 2008, 13, 693.

57 3 Protein-Selective ydrolysis of Amides Summary of This Section Mb- or PDF-selective artificial protease AmPs-selective artificial protease Conventional methods can t get these fruits. J. Suh et al., J. Biol. Inorg. Chem. 2008, 13, 693.