A Thymine-PNA Monomer as New Isocyanide Component in the Ugi Reaction: A Direct Entry to PNA Dimers

Abstract

A new PNA monomer was synthesized for use as the ­isocyanide component in a Ugi condensation in order to produce peptide nucleic acid (PNA) dimers also labelled with Cr(CO)₃.

Key words

multicomponent reaction - arene complexes - chromiumtricarbonyl - peptide nucleic acid - isocyanide

References

• 1a Dömling A. Ugi I. Angew. Chem. Int. Ed.  2000,  39:  3168 
• 1b Ugi I. Pure Appl. Chem.  2001,  73:  187 
• 1c Dömling A. Curr. Opin. Chem. Biol.  2002,  6:  306 
• 1d Weber L. Curr. Med. Chem.  2002,  9:  2086 
• 1e Hulme C. Gore V. Curr. Med. Chem.  2003,  10:  51 
• 1f Zhu J. Eur. J. Org. Chem.  2003,  1133 
• 1g Henkel B. Sax M. Dömling A. Tetrahedron Lett.  2003,  44:  7015 
• 1h Kusebauch U. Beck B. Messer K. Herdtweck E. Dömling A. Org. Lett.  2003,  5:  4021 
• 2a Shibata N. Kumar Das B. Takeuchi Y. J. Chem. Soc., Perkin Trans. 1  2002,  197 
• 2b Kazmaier U. Hebach C. Synlett  2003,  1591 
• 2c Ziegler T. Gerlin S. Lang M. Angew Chem. Int. Ed.  2000,  30:  2109 
• 3a Nielsen PE. Egholm M. Peptide Nucleic Acids. Protocols and Applications   Horizon Scientific Press; Wymondham, Norfolk, UK: 1999. 
• 3b Antsypovitch SI. Russ. Chem. Rev.  2002,  71:  71 
• 3c Irgolic KJ. In Houben-Weyl   4th ed., Vol. E12b:  Klamann D. Thieme; Stuttgart: 1990.  p.150 
• 4a Maison W. Schlemminger I. Westerhoff O. Martens J. Bioorg. Med. Chem. Lett.  2000,  8:  1343 
• 4b Shibata N. Das BK. Honjo H. Takeuchi Y. J. Chem. Soc., Perkin Trans. 1  2001,  1605 
• 5a Dömling A. Bioorg. Med. Chem. Lett.  1999,  9:  2871 
• 5b The same reaction was recently repeated by: Xu P. Zhang T. Wang W. Zou X. Zhan X. Fu Y. Synthesis  2003,  1171 
• 6 Baldoli C. Maiorana S. Licandro E. Zinzalla G. Perdicchia D. Org. Lett.  2002,  24:  4341 
• 8 For the effect on binding properties of substituents at glycine α-carbon in PNA oligomers see: Püschl A. Sforza S. Haaima G. Dahl O. Nielsen PE. Tetrahedron. Lett.  1998,  39:  4707 
• 9a Severin K. Bergs R. Beck W. Angew. Chem. Int. Ed.  1998,  37:  1634 
• 9b Jaouen G. Salmain M. Vessieres A. Varenne A. Brossiers P. J. Organomet.Chem.  1999,  589:  92 
• 9c Metzler-Nolte N. Angew. Chem. Int. Ed.  2001,  40:  1040 
• 9d Metzler-Nolte N. Verheijen JC. van der Marel G. van Boom JH. Bioconjugate Chem.  2000,  11:  741 
• 9e Metzler-Nolte N. van Staveren DR. Chem. Commun.  2002,  1406 
• 9f Baldoli C. Maiorana S. Licandro E. Vandoni B. Perdicchia D. Giannini C. Salmain M. J. Mol. Catal. A: Chem.  2003,  203-204:  165 
• 10 The use of a Ugi condensation to obtain tungsten carbonyl complexes of amino acids has been recently reported : Kernbach U. Mühl M. Polborn K. Fehlammer WP. Jaouen G. Inorg. Chim. Acta  2002,  334:  45 
• 11 Corradini R. Nielsen P. Tedeschi T. Marchelli R. Pushl A. Tetrahedron: Asymmetry  2002,  13:  1629 
• 13 The synthesis of isocyano dipeptides has been recently reported: Zhao G. Bughin C. Bienaymé H. Zhu J. Synlett  2003,  1153 
• 14 Uhlmann E. Peyman A. Breipohl G. Will DW. Angew. Chem. Int. Ed.  1998,  37:  2796 
• 15 Duczek W. Deutsch J. Vieth S. Niclas H.-J. Synthesis  1996,  37 
• 17 Ugi I. Fetzer U. Eholzer U. Knupfer H. Offermann K. Angew. Chem., Int. Ed. Engl.  1965,  4:  472 

7

For compounds 4a-d see ref. [6] ; compound 4e: yield: 15%, 60:40 diastereoisomeric ratio; Diast. I: R_f = 0.51 (EtOAc). Mp 142 °C dec. (pentane). Anal. Calcd for C₃₅H₃₁CrFN₆O₁₂: C, 52.64; H, 3.91; N, 10.52. Found: C, 52.70; H, 3.88; N, 10.50. ¹H NMR (300 MHz, CDCl₃): δ = 1.84 (s, 3 H, CH₃), 3.36-3.54 (m, 2 H, NCH₂CH₂N), 3.82 (s, 3 H, OCH₃), 3.88-4.13 (m, 3 H, NCH₂CH₂N + CH₂CO), 4.69 (s, 1 H, CH), 4.74-4.79 (m, 1 H, CH₂CO), 4.92-5.05 [m, 3 H, PhCr(CO)₃ + CH₂O], 5.30-5.39 [m, 1 H, PhCr(CO)₃], 5.43 [dd, 1 H, J ₁ = J ₂ = 6.1 Hz, PhCr(CO)₃], 5.73 (s, 1 H, NH), 6.01 [m, 2 H, PhCr(CO)₃], 6.50 (s, 1 H, CH=), 7.19 (dd, 1 H, J = 2.4, 9.0 Hz, arom.), 7.28-7.42 (m, 5 H, Ph), 7.60 (d, 1 H, J = 2.4 Hz, arom.), 8.30 (s, 1 H, NH), 8.59 (d, 1 H, J = 9.0 Hz, arom.), 10.51 (s, 1 H, NH). IR (nujol): 1967, 1905, 1881, 1692-1672 cm^-1. Diast. II: R_f = 0.31 (EtOAc), eluted as a mixture of complexed and uncomplexed monomer. ¹H NMR (CDCl₃): δ = 1.80 (s, 3 H, CH₃), 3.34-3.46 (m, 4 H, NCH₂CH₂N), 3.83 (s, 3 H, OCH₃), 4.43-4.55 (m, 3 H, CH₂CO + CH), 5.08-5.11 [m, 4 H, PhCr(CO)₃ + CH₂O], 5.84-5.93 [m, 3 H, PhCr(CO)₃ + NH], 6.70 (s, 1 H, CH=), 7.05-7.62 (m, 7 H, Ph + arom.), 8.56 (s broad, 2 H, arom. + NH), 10.54 (s, 1 H, NH). IR (nujol): 1975, 1894, 1680 cm^-1.

12

Further experiments are in progress in order to rationalize this behaviour and clarify the role of the substituent, using a series of meta-substituted complexed and uncomplexed monomers.

16

Compound 10: The trifluoroacetate salt 9 (3.0 mmol) and cyanomethyl formate (3.0 mmol) were dissolved in CH₂Cl₂ (25 mL) and cooled in an ice-bath to 0 °C. Then, a solution of DIEA (3.66 mmol) in CH₂Cl₂ (5 mL) was added. The solution was stirred for 2 h at 20 °C. After evaporation of the solvent, the crude product was purified by column chromatography (eluent: EtOAc:MeOH, 6:4, R_f = 0.36) affording compound 10, as white solid, in 94% yield. Mp 62-63 °C (pentane). Anal. Calcd for C₁₃H₁₈N₄O₆ (326.3): C, 47.85; H, 5.56; N, 17.17. Found: C, 47.98; H, 5.54; N, 17.17. ¹H NMR (300 MHz, CD₃OD) two rotamers I/II in a 60:40 ratio are present: δ = 1.87 (s, 3 H, CH₃), 3.34-3.72 (m, 4 H, NCH₂CH₂), 3.72 (s, 3 H, OCH₃, I rot.), 3.80 (s, 3 H, OCH₃, II rot.), 4.14 (s, 2 H, NCH ₂ COOCH₃, I rot.), 4.34 (s, 2 H, NCH ₂ COOCH₃, II rot.), 4.55 (s, 2 H, NCH₂CO, II rot.), 4.73 (s, 2 H, NCH₂CO, II rot.), 7.26 (s, 1 H, CH=, II rot.), 7.31 (s, 1 H, CH=, I rot.), 8.02 (s, 1 H, NCHO, II rot.), 8.15 (s, 1 H, NCHO, rot). ¹³C NMR (75 MHz, CD₃OD, I + II rot.): δ = 12.2, 36.6, 37.0, 52.8, 53.20, 143.6, 143.8, 153.0, 163.4, 164.3, 164.8, 167.0, 167.5, 169.9, 170.3, 171.4, 171.5, 171.6. MS (FAB⁺): m/z = 349 [M + Na⁺]. IR (nujol): 1852-1720 cm^-1.

18

The reaction has not yet been optimized. Compound 6: mp 178-180 °C (pentane). Anal. Calcd for C₁₃H₁₆N₄O₅ (308.3): C, 50.48; H, 5.54; N, 18.11. Found: C, 50.40; H, 5.53; N, 18.13. ¹H NMR (300 MHz, CDCl₃), rotamers I/II, 60:40: δ = 1.93 (s, 3 H, CH₃), 3.48-3.79 (m, 4 H, NCH₂CH₂), 3.84 (s, 3 H, OCH₃), 4.14 (s, 2 H, CH ₂CO₂CH₃, I rot.), 4.33 (s, 2 H, CH ₂CO₂CH₃, II rot.), 4.45 (s, 2 H, NCH₂CO, I rot.), 4.66 (s, 2 H, NCH₂CO, II rot.), 6.99 (s, 1 H, CH=, I rot.), 7.04, (s, 1 H, CH=, II rot.). ¹³C NMR (75 MHz, DMSO, I + II rot.): δ = 12.1, 12.4, 46.5, 47.8, 47.9, 48.2, 58.8, 51.9, 52.4, 108.4, 142.0, 142.1, 151.0, 164.4, 167.8, 168.4, 169.4, 169.9. MS (EI): m/z = 308 (M⁺). IR (nujol ): 1650-1744 (CO), 2153 (NC) cm^-1.

19

An equimolar mixture of imine 11 (0.3 mmol.), 1-carboxy methylthymine 2 and isonitrile 6 in dry MeOH (1 mL) was heated under nitrogen at 60 °C for 5 min, and then stirred at r.t. for 2 d. After evaporation of the solvent, the crude mixture was purified by column chromatography (eluent: EtOAc:MeOH, 9:1, R_f = 0.31). Compound 12: 51% yield white solid, mp 158-160 °C (pentane). Anal. Calcd for C₃₇H₄₂N₈O₁₁: C, 57.36; H, 5.46; N, 14.46. Found: C, 57.40; H, 5.45; N, 14.50. ¹H NMR (300 MHz, CDCl₃), rotamers I/II, 60:40: δ = 1.73-1.87 (m, 6 H, CH₃), 2.98-3.57 (m, 8 H, NCH₂CH₂N), 3.64 (s, 3 H, OCH₃, II rot.), 3.68 (s, 3 H, OCH₃, I rot.), 3.90-4.72 (m, 6 H, NCH ₂CO₂CH₃, NCH ₂CO), 5.01-5.13 (m, 2 H, OCH₂Ph), 5.59 (s, 1 H, CH, II rot.), 5.78 (s, 1 H, CH, I rot.), 5.95 (s, 1 H, NH, I rot.), 6.01 (s, 1 H, NH, II rot.), 6.67 (s, 1 H, CH=, I rot.), 6.73 (s, 1 H, CH=, II rot.), 6.98 (s, 1 H, CH=, II rot.), 7.03 (s, 1 H, CH=, I rot.), 7.24-7.35 (m, 10 H, Ph), 9.35 (br s, 1 H, NH). ¹³C NMR (75 MHz, CDCl₃, I + II rot.): δ = 12.2, 37.5, 40.0, 44.7, 47.9, 48.2, 48.4, 48.9, 52.5, 52.8, 64.1, 66.9, 110.2, 110.4, 128.3, 128.5, 129.2, 129.9, 133.1, 136.5, 141.2, 141.7, 151.2, 151.4, 151.5, 156.7, 164.4, 164.5, 167.9, 168.3, 170.7. MS (HRMS, ESI): calcd. for C₃₇H₄₂N₈O₁₁: 774.2973; found: 775.3173 [M + H⁺], 797.2903 [M + Na⁺]. IR (nujol): 1675, b (CO) cm^-1.

20

General Procedure for the Synthesis of 13a-d: An equimolar mixture of imines 1a-d (0.3 mmol.), 1-carboxy methylthymine 2 and isonitrile 6 in dry MeOH (1 mL) was heated under nitrogen at 45 °C for 24 h. After evaporation of the solvent, the crude mixture was purified by column chromatography. Compound 13a: 68% yield (eluent: EtOAc:MeOH, 95:5, R_f = 0.42), yellow-green solid, mp 176-179 °C (pentane). Anal. Calcd for C₄₀H₄₂CrN₈O₁₄: C, 52.75; H, 4.65; N, 12.30. Found: C, 52.70; H, 4.61; N, 12.32. ¹³C NMR, (125 MHz, CD₃OD), I+II rot.: δ = 12.3, 12.4, 12.6, 12.7, 14.0, 38.4, 38.7, 40.8, 43.2, 44.8, 45.9, 49.9, 49.7, 64.4, 65.2, 67.6, 67.9, 91.1, 91.4, 97.9, 98.2, 98.4, 99.7, 110.6, 110.8, 129.1, 129.5, 130.2, 131.3, 135.3, 138.2, 143.6, 143.8, 144.0, 151.4, 153.1, 166.9, 169.3, 169.9, 170.3, 171.4, 172.0, 233.9. MS (ESI, HOAc): 1032.3 [M + 2 H + +2 HOAc], 933.2 [M + Na]⁺. IR (nujol): 1966, 1886, 1664 cm^-1. Compound 13b: yellow solid (30%), dr 1:1, (eluent: EtOAc:MeOH, 9:1, R_f: diast. I = 0.62, diast. II = 0.55). ¹³C NMR (125 MHz, CDCl₃): δ = 10.7, 36.9, 39.0, 39.5, 44.2, 46.9, 47.0,47.2, 51.3, 54.7, 58.6, 66.1, 109.1, 109.3, 110.9, 118.6, 120.5, 121.6, 127.5, 127.9, 130.5, 135.6, 142.4, 142.6, 151.7, 162.0, 165.6, 168.4, 171.6, 232.8. Anal. Calcd for C₄₁H₄₄CrN₈O₁₅: C, 52.34; H, 4.71; N, 11.91. Found: C, 52.32; H, 4.70; N, 11.90. ESI-MS: 962.9 [M + Na]⁺. IR (nujol): 1974, 1883, 1681 cm^-1. Compound 13c: 53% yield, dr 1:1 (eluent: EtOAc + 5% of MeOH, Rf: diast. I = 0.44, diast. II = 0.38). Anal. Calcd for C₄₁H₄₄CrN₈O₁₄: C, 53.75; H, 4.80; N, 12.12. Found: C, 53.68; H, 4.81; N, 12.10. ¹³C NMR (125 MHz, CDCl₃): δ = 11.9, 13.5, 18.7, 28.4, 34.8, 37.19, 37.4, 38.1, 39.8, 40.2, 41.6, 41.8, 43.2, 43.4, 43.6, 43.8, 47.5, 47.8, 48.1, 48.3, 48.6, 48.8, 49.1,49.3, 49.4, 49.6, 49.7, 49.9, 50.0, 50.3, 50.6, 52.3, 52.7, 59.0, 66.6, 66.9, 86.2, 90.8, 91.6, 95.8, 96.6, 97.4, 109.9, 110.2, 110.5, 110.6, 126.5, 127.9, 128.0, 128.3, 128.5, 128.8, 129.5, 130.8, 131.1, 136.2, 138.6, 140.7, 140.9, 141.3, 150.8, 151.3, 156.4, 164.3, 167.7, 168.1, 168.3, 168.6, 170.6, 171.1, 231.4, 231.7, 232.8. MS (HRMS, ESI): calcd for C₄₁H₄₄CrN₈O₁₄: 924.2382; found: 947.2297 [M + Na⁺]. IR (nujol): 1965, 1885, 1664 cm^-1. Compound 13d: green solid, 28% yield, dr 1:1 (eluent: EtOAc:MeOH, 8/2 R_f : diast. I = 0.43, diast. II = 0.37). Anal. Calcd for C₄₀H₄₁ClCrN₈O₁₄: C, 50.83; H, 4.37; N, 11.85. Found: C, 50.78; H, 4.35; N, 11.85. ¹³C NMR (125 MHz, CDCl₃): δ = 12.9, 13.5, 38.1, 39.7, 40.2, 41.8, 43.4, 43.7, 48.2, 52.7, 54.7, 66.6, 66.8, 90.9, 91.7, 95.8, 96.7, 97.4, 110.5, 110.7, 126.5-129.5, 140.3, 140.9, 150.7, 151.1, 151.3, 164.3, 164.5, 167.5, 168.2, 168.4, 172.0, 231.7, 231.9. ESI-MS: m/z = 967.1 [M + Na]⁺. IR (nujol): 1977, 1938, 1912, 1682 cm^-1.

21

General Procedure for the Ester Hydrolysis in Compounds 13a-d: LiOH (0.11 mmol, 5 equiv) was added to a solution of 13a-d (1 equiv) in MeOH (3 mL) and the mixture stirred for 6 h at r.t. (TLC, eluent: EtOAc:MeOH, 8:2, R_f = 0.1). H₂O (5 mL) was added and the solution treated with KHSO₄ (0.8 mL of 1 M solution). After extraction with EtOAc (3 × 10 mL) the crude solid product was suspended in pentane and filtered. Selected data for 14a-d. Compound 14a: light-green solid, mp 205 °C (dec.). Anal. Calcd for C₃₉H₄₀CrN₈O₁₄: C, 52.23; H, 4.50; N, 12.50. Found: C, 52.12; H, 4.48; N, 12.51. ESI-MS: m/z = 895.2 [M - H]^-. IR (nujol): 1966, 1891, 1669 cm^-1. Compound 14b: light-green solid. Anal. Calcd for C₄₀H₄₂CrN₈O₁₅: C, 51.84; H, 4.57; N, 12.09. Found: C, 51.82; H, 4.58; N, 12.10. ESI-MS: m/z = 925.1 [M - H]^-. IR (nujol): 1964, 1881, 1686 cm^-1. Compound 14c: light-green solid. Anal. Calcd for C₄₀H₄₂CrN₈O₁₄: C, 52.75; H, 4.65; N, 12.30. Found: C, 52.13; H, 4.67; N, 12.31. ¹³C NMR (75 MHz, DMSO): 11.7, 12.1, 13.4, 18.0, 18.5, 21.0, 28.8, 26.2, 36.2, 37.0, 37.4, 42.7, 43.5, 46.1, 46.6, 47.8, 48.6, 49.2, 65.4, 65.6, 89.6, 93.4, 97.5, 107.7, 108.0, 112.8, 126.2, 127.7, 128.2, 137.0, 142.1, 142.3, 148.9, 150.9, 156.0, 161.7, 164.3, 166.9, 167.3, 167.6, 168.1, 172.0, 233.7, 233.2. ESI-MS: m/z = 909.2 [M - H]^-, 933.4 [M + Na]⁺. IR (nujol): 1966, 1889, 1669 cm^-1. Compound 14d: light-green solid. Anal. Calcd for C₃₉H₃₉ClCrN₈O₁₄: C, 50.30; H, 4.22;N, 12.03. Found: C, 50.20; H, 4.20; N, 12.00. ESI-MS: m/z = 928.9 [M - H]^-. IR (nujol): 1977, 1912, 1680 cm^-1.