Design, Synthesis, Conformational Analysis and Application of Azabicyclo­alkane Amino Acids as Constrained Dipeptide Mimics

Abstract

In the field of peptidomimetics, major efforts have been focused on the design and synthesis of conformationally constrained compounds that mimic or induce reverse-turn motifs of peptides and proteins which are thought to play important roles in recognition and biological activity. In this regard, a particularly attractive class of compounds are the azabicyclo[X.Y.0]alkane dipeptide mimics. We present our efforts on the design, synthesis, and conformational analysis of a series of rigid surrogates of dipeptide units for applications within constrained peptide analogues, for employment as inputs for combinatorial science and biological applications. Several general and versatile synthetic approaches have been conceived to deliver a variety of enantiomerically pure azabicycloalkanes. All of these methodologies rely on the construction of a 5-, 6-, or 7-membered lactam on a preformed proline based nucleus. Different strategies were adopted to perform the key cyclization step: a) radical addition to an olefinic double bond, b) alkylation of a malonate enolate, c) ring-closing metathesis (RCM), and d) lactam bond formation.

• 1 Introduction

• 2 Synthesis of Azabicyclo[X.Y.0]alkane Amino Acids

• 2.1 Radical Approach

• 2.1.1 Synthesis of Cyclization Precursors

• 2.2 Non-Radical Approaches

• 2.2.1 Synthesis of 5,5-, 6,5- and 7,5-Fused Bicyclic Lactams via Horner-Emmons Olefination and Lactam Bond Formation

• 2.2.2 Hydrophobic Appendages at C-3 Position via Malonate Alkylation or RCM

• 2.2.3 Spiro and Trinuclear Dipeptide Mimics via Lactam Bond Formation or RCM

• 2.2.4 Heteroatomic Side-Chain Functionalization via Lactam Bond Formation or RCM

• 3 Conformational Analysis of Azabicycloalkane Amino ­Acids

• 3.1 Molecular Modeling

• 3.2 Discussion of ¹H NMR and IR Data

• 4 Incorporation of Azabicycloalkane Amino Acids into ­Bioactive Peptides

• 4.1 Thrombin Inhibitors

• 4.2 α_νβ₃-Integrin Ligands

peptidomimetic - peptide secondary structure - azabicycloalkane amino acids - biological activity - conformational analysis

References

Recent reviews for design and synthesis of ‘dipeptide-turn mimetics’:

1a Halab L. Gosselin F. Lubell WD. Biopolym. (Pept. Sci.)  2000,  55:  101 

1b Hanessian S. McNaughton-Smith G. Lombart H.-G. Lubell WD. Tetrahedron  1997,  53:  12789 

1c Reviews for the applications of peptidomimetics including turn mimetics: Giannis A. Kolter T. Angew. Chem., Int. Ed. Engl.  1994,  33:  1699 

Reviews regarding conformational and topographical considerations in designing peptidomimetics including turn mimetics:

2a Hruby VJ. Life Sci.  1982,  31:  189 

2b Hruby VJ. Al-Obeidi F. Kazmierski WM. Biochem. J.  1990,  268:  249 

2c Hruby VJ. Balse PM. Curr. Top. Med. Chem.  2000,  7:  945 

Indolizidin-2-one amino acids:

3a Hanessian S. Ronan B. Laoui A. Bioorg. Med. Chem. Lett.  1994,  4:  1397 

3b Li W. Hanau CE. d’Avignon A. Moeller KD. J. Org. Chem.  1995,  60:  8155 

3c Hanessian S. McNaughton-Smith G. Bioorg. Med. Chem. Lett.  1996,  6:  1567 

3d Li W. Moeller KD. J. Am. Chem. Soc.  1996,  118:  10106 

3e Wessig P. Tetrahedron Lett.  1999,  40:  5987 

3f Boatman PD. Ogbu CO. Eguchi M. Kim H.-O. Nakanishi H. Cao B. Shea JP. Kahn M. J. Med. Chem.  1999,  42:  1367 

3g Estiarte MA. Rubiralta M. Diez A. Thormann M. Giralt E. J. Org. Chem.  2000,  65:  6992 

3h Mulzer J. Schulzchen F. Bats J.-W. Tetrahedron  2000,  56:  4289 

3i Beal LM. Liu B. Chu W. Moeller KD. Tetrahedron  2000,  56:  10113 

3j Wang W. Xiong C. Hruby VJ. Tetrahedron Lett.  2001,  42:  3159 

3k Zhang X. Jiang W. Schmitt AC. Tetrahedron Lett.  2001,  42:  4943 

3l Millet R. Domarkas J. Rombaux P. Rigo B. Houssin R. Hénichart J.-P. Tetrahedron Lett.  2002,  43:  5087 

3m Zhang J. Xiong C. Wang W. Ying J. Hruby VJ. Org. Lett.  2002,  4:  4029 

3n Sun H. Moeller KD. Org. Lett.  2002,  4:  1547 

3o Wang W. Yang J. Ying J. Xiong C. Zhang J. Cai C. Hruby VJ. J. Org. Chem.  2002,  67:  6353 

3p Zhang J. Xiong C. Ying J. Wang W. Hruby VJ. Org. Lett.  2003,  5:  3115 

3q Gardiner J. Abell AD. Tetrahedron Lett.  2003,  44:  4227 

Indolizidin-9-one:

4a Gosselin F. Lubell WD. J. Org. Chem.  1998,  63:  7463 

4b De La Figuera N. Rosas I. Garcia-Lopez MT. Gonzalez-Muniz R. J. Chem. Soc., Chem. Comm.  1994,  613 

4c Lamazzi C. Carbonnel S. Calinaud P. Troin Y. Heterocycles  2003,  60:  1447 

4d Shimizu M. Nemoto H. Kakuda H. Takahata H. Heterocycles  2003,  59:  245 

Pyrroloazepinone amino acids:

5a Tremmel P. Geyer A. J. Am. Chem. Soc.  2002,  124:  8548 

5b Gosselin F. Lubell WD. J. Org. Chem.  2000,  65:  2163 

5c Geyer A. Moser F. Eur. J. Org. Chem.  2000,  1113 

Other examples:

6a Robl JA. Tetrahedron Lett.  1994,  35:  393 

6b Robl JA. Cimarusti MP. Simpkins LM. Weller HN. Pan YY. Malley M. Di Marco JD. J. Am. Chem. Soc.  1994,  116:  2348 

6c Robl JA. Karanewsky DS. Asaad MM. Tetrahedron Lett.  1995,  36:  1593 

6d Mueller R. Revesz L. Tetrahedron Lett.  1994,  35:  4091 

6e De Lombaert S. Blanchard L. Stamford LB. Sperbeck DM. Grim MD. Jenson TM. Rodriguez HR. Tetrahedron Lett.  1994,  35:  7513 

6f Lombart HG. Lubell WD. J. Org. Chem.  1994,  59:  6147 

6g Nagai U. Sato K. Nakamura R. Kato R. Tetrahedron  1993,  49:  3577 

7 Colombo L. Di Giacomo M. Papeo G. Cargo O. Scolastico C. Manzoni L. Tetrahedron Lett.  1994,  35:  4031 

8 Colombo L. Di Giacomo M. Scolastico C. Manzoni L. Belvisi L. Molteni V. Tetrahedron Lett.  1995,  36:  625 

9 Colombo L. Di Giacomo M. Belvisi L. Manzoni L. Scolastico C. Gazz. Chim. Ital.  1996,  126:  543 

10 Manzoni L. Belvisi L. Scolastico C. Synlett  2000,  1287 

11 Baldwin EJ. J. Chem. Soc., Chem. Commun.  1976,  734 

Calculations were performed employing a modified version of the MM2 force field model for intramolecular radical addition to alkenes developed by Houk and now incorporated in the program MacroModel. See:

12a Belvisi L. Gennari C. Poli G. Scolastico C. Salom B. Vassallo M. Tetrahedron  1992,  48:  3945 

12b Houk KN. Paddon-Row MN. Spellmeyer DC. Rondan G. Nagase S. J. Org. Chem.  1987,  52:  959 

12c Mohamadi F. Richards NGJ. Guida WC. Liskamp R. Caufield C. Chang G. Hendrickson T. Still WC. J. Comput. Chem.  1990,  11:  440 

13 Viehe HG. Merény R. Stella L. Janousek Z. Angew. Chem., Int. Ed. Engl.  1979,  18:  917 

14a Cignarella G. Nathansohon G. J. Org. Chem.  1961,  26:  1500 

14b Boutelje J. Hjalmarsson M. Hult K. Lindbäck M. Norin T. Bioorg. Chem.  1988,  16:  364 

15 Peterson JS. Felles G. Rapoport H. J. Am. Chem. Soc.  1984,  106:  4539 

16 Chiesa MV. Manzoni L. Scolastico C. Synlett  1996,  441 

17 Greco PA. Jaw JY. Claremond DA. Nicolaou KC. J. Org. Chem.  1981,  46:  1215 

18a Lombart H.-G. Lubell WD. J. Org. Chem.  1996,  61:  9437 

18b Polyak F. Lubell WD. J. Org. Chem.  1998,  63:  7463 

18c Polyak F. Lubell WD. J. Org. Chem.  2001,  66:  1171 

19 Dietrich E. Lubell WD. J. Org. Chem.  2003,  68:  6988 

20 Angiolini M. Araneo S. Belvisi L. Cesarotti E. Checchia A. Crippa L. Manzoni L. Scolastico C. Eur. J. Org. Chem.  2000,  2571 ; the procedures reported in this paper have been also used for the gram scale preparation of the bicyclic lactams

21 Collado I. Ezquerra J. Vaquero JJ. Pedregal C. Tetrahedron Lett.  1994,  43:  8037 

22 Schmidt U. Lieberkneckt A. Wild J. Synthesis  1984,  53 

23a Salimbeni A. Paleari F. Canevotti R. Criuscuoli M. Lippi A. Angiolini M. Belvisi L. Scolastico C. Colombo L. Bioorg. Med. Chem. Lett.  1997,  7:  2205 

23b Colombo L. Di Giacomo M. Brusotti G. Sardone N. Angiolini M. Belvisi L. Maffioli S. Manzoni L. Scolastico C. Tetrahedron  1998,  54:  5325 

24

Steward, J. J. P. MOPAC Version 60, F. J. Seiler Research Laboratory U. S. Air Force Academy CO 80840, QCPE 455.

25 Högberg T. Ström P. Ebner M. Rämsby SJ. J. Org. Chem.  1987,  52:  2033 

26 Kajigaeshi S. Asano K. Fujisaki S. Kakinami T. Okamoto T. Chem. Lett.  1989,  463 

27 Colombo L. Di Giacomo M. Vinci V. Colombo M. Manzoni L. Scolastico C. Tetrahedron  2003,  59:  4501 

For reviews on catalytic olefin metathesis see:

28a Grubbs RH. Chang S. Tetrahedron  1998,  54:  4413 

28b Phillips AJ. Abell AD. Aldrichimica Acta  1999,  32:  75 

28c Fürstner A. Angew. Chem. Int. Ed.  2000,  39:  3012 

28d Trnka TM. Grubbs RH. Acc. Chem Res.  2001,  34:  18 

28e Hoveyda AH. Schrock RR. Chem.-Eur. J.  2001,  7:  945 

29 Grossmith CE. Senia F. Wagner J. Synlett  1999,  1660 

30a Beal LM. Moeller KD. Tetrahedron Lett.  1998,  39:  4639 

30b Beal LM. Liu B. Chu W. Moeller KD. Tetrahedron  2000,  56:  10113 

30c Hoffmann T. Lanig H. Waibel R. Gmeiner P. Angew. Chem. Int. Ed.  2001,  40:  3361 

30d Sung H. Sunghoon M. Beak P. J. Org. Chem.  2001,  66:  9056 

31 Brocherieux-Lanoy S. Dhimane H. Poupon J.-C. Vanucci C. Lhommet G. J. Chem. Soc., Perkin Trans. 1  1997,  2163 

32 Shono T. Fujita T. Matsumura Y. Chem. Lett.  1991,  1:  81 

33a Berkovitz DB. McFadden JM. Chisowa E. Semerad CL. J. Am. Chem. Soc.  2000,  122:  11031 

33b Berkovitz DB. McFadden JM. Sloss MK. J. Org. Chem.  2000,  65:  2907 

33c Berkovitz DB. Chisowa E. McFadden JM. Tetrahedron  2001,  57:  6329 

34

The following activating agents were used in different conditions of temperature and solvent: DCC CIP/HOAt HATU EDC/HOAt DPPA and PyBop.

35 Frérot E. Coste J. Pantaloni A. Dufour M.-N. Jouin P. Tetrahedron  1991,  47:  259 

36a Scholl M. Ding S. Lee CW. Grubbs RH. Org. Lett.  1999,  1:  953 

36b Chatterjee AK. Grubbs RH. Org. Lett.  1999,  1:  1751 

37 Garber SB. Kingsbury JS. Gray BL. Hoveyda AH. J. Am. Chem. Soc.  2000,  122:  8168 

38 Manzoni L. Colombo M. May E. Scolastico C. Tetrahedron  2001,  57:  249 

39 Belvisi L. Colombo L. Colombo M. Di Giacomo M. Manzoni L. Vodopivec B. Scolastico C. Tetrahedron  2001,  57:  6463 

40 Crossley MJ. Reid RC. J. Chem. Soc., Chem. Commun.  1994,  2237 

41a For a review on pyroglutamic acids see: Nájera C. Yus M. Tetrahedron: Asymmetry  1999,  10:  2245 ; and references cited therein

41b Shono T. Matsumura Y. Tsubata K. Sugihara Y. Yamane S.-I. Kanazawa T. Aoki T. J. Am. Chem. Soc.  1982,  104:  6697 

41c Shono T. Matsumura Y. Tsubata K. Org. Synth.  1985,  63:  206 

42 Ezquerra J. Pedregal C. Rubio A. J. Org. Chem.  1994,  59:  4327 ; and references therein

43a Pedregal C. Ezquerra J. Escribano A. Carreño MC. Garcia Ruano JL. Tetrahedron Lett.  1994,  35:  7277 

43b Ezquerra J. Pedregal C. Yruretagoyena B. Rubio A. Carreño MC. Escribano A. Garcia Ruano J. J. Org. Chem.  1995,  60:  2925 

44a Russowsky D. Petersen RZ. Godoi MN. Pilli RA. Tetrahedron Lett.  2000,  41:  9939 

44b Onishi Y. Ito T. Ysuda M. Baba A. Eur. J. Org. Chem.  2002,  1578 

45 Hanessian S. Margarita R. Tetrahedron Lett.  1998,  39:  5887 

46a Hayen A. Kock R. Saak W. Haase D. Metzger JO. J. Am. Chem. Soc.  2000,  122:  12458 

46b Mathias LJ. Synthesis  1979,  561 

47a Artale E. Banfi G. Belvisi L. Colombo L. Colombo M. Manzoni L. Scolastico C. Tetrahedron  2003,  59:  6241 

47b Bracci A. Manzoni L. Scolastico C. Synthesis  2003,  2363 

48 McClure KF. Renold P. Kemp DS. J. Org. Chem.  1995,  60:  454 

49 Rose GD. Gierasch LM. Smith JA. Adv. Prot. Chem.  1985,  37:  1 

50 Chang G. Guida WC. Still WC. J. Am. Chem. Soc.  1989,  11:  4379 

51 Still WC. Tempczyk A. Hawley RC. Hendrickson T. J. Am. Chem. Soc.  1990,  112:  6127 

52 Garcia-Moreno EB. Dwyer JJ. Gittis AG. Lattman EE. Spencer DS. Sites WE. Biophys. Chem.  1997,  64:  211 

53 Belvisi L. Bernardi A. Manzoni L. Potenza D. Scolastico C. Eur. J. Org. Chem.  2000,  2563 

54

Molecular mechanics calculations were performed within the framework of MacroModel [12c] version 55 using the MacroModel implementation of the Amber all-atom force field [77] (denoted AMBER*). The torsional space of each molecule was randomly varied with the usage-directed Monte Carlo conformational search of Chang Guida and Still. [50] Ring-closure bonds were defined in the six- and seven-membered rings of the 6,5- and 7,5-fused bicyclic lactams, respectively. Amide bonds were included among the rotatable bonds. For each search at least 2000 starting structures for each variable torsion angle were generated and minimized until the gradient was less than 0.05 kJ/Åmol using the truncated Newton-Raphson method [78] implemented in MacroModel. Duplicate conformations and those with an energy greater than 6 kcal/mol above the global minimum were discarded. The nature of the stationary points individuated was tested by computing the eigenvalues of the second-derivative matrix.

55 Ball JB. Hughes RA. Alewood PF. Andrews PR. Tetrahedron  1993,  49:  3467 

56

Values of the Cα _i -Cα _{ι + 3} distance (dα) of less than 7 Å were used to define the presence of a reverse-turn. The range 0±30° for the virtual torsion angle β (C _i -Cα _i+1 -Cα _i+2 -N _i+3 ) was taken to indicate a tight reverse-turn. [55] Assignment of a low-energy conformation to a particular turn type was made where possible on the basis of the ideal φ and ψ torsion angles (±30°) reported by Rose et al. [49] With regard to the intramolecular hydrogen bond parameters it was assumed that a hydrogen bond is formed when the distance between the acceptor and the hydrogen of the donor is smaller than 25 Å, the N-H···O bond angle is greater than 120°, and the H···O=C angle is greater than 90°.

57a Takeuchi Y. Marshall GR. J. Am. Chem. Soc.  1998,  120:  5363 ; and references therein

57b Gillespie P. Cicariello J. Olson GL. Biopolymers  1997,  43:  191 

58

The percentage of β-turn hydrogen bond resulting from Monte Carlo/Stochastic Dynamics (MC/SD) [79] simulations in GB/SA chloroform or water of dipeptide and tetrapeptide analogues of the indolizidinone ring system is generally lower than the corresponding value calculated by the MC/EM protocol. A better agreement between the two computational approaches is observed for the benzyl-substituted dipeptide mimic 59x and its longer derivatives. [59] It should be also noted that MC/SD simulations of some bicyclic systems showed convergence problems. NMR and IR spectroscopic studies of sequences of different length will play an important part in assessing the β-turn inducing potential of the bicyclic mimics.

59a Belvisi L. Gennari C. Mielgo A. Potenza D. Scolastico C. Eur. J. Org. Chem.  1999,  389 

59b Belvisi L. Gennari C. Madder A. Mielgo A. Potenza D. Scolastico C. Eur. J. Org. Chem.  2000,  5:  695 

60

Previous data [59] suggest that δNH < 62 ppm for a completely non-hydrogen-bonded peptide amide or carbamate proton.

61a Gellman SH. Dado GP. Liang GB. Adams RB. J. Am. Chem. Soc.  1991,  113:  1164 

61b Gellman SH. Desper JM. Liang GB. J. Am. Chem. Soc.  1993,  115:  925 

62

The amide I region of the IR spectrum is predominately due to the C=O stretching vibration; 35y, 37y, 40y, and 42y have three different types of carbonyls: a secondary amide, a tertiary amide, and a carbamate. On the basis of model compounds, [80] they are known to give rise to three distinct absorbances: at 1680-1675 cm^{- 1} for the free secondary amide, at 1665 cm^{- 1} for the free tertiary amide of the 6,5-fused bicyclic lactam, and at 1730 cm^{- 1} for the free carbamate. Hydrogen bonding to the carbonyl shifts the band to lower frequency by 20-30 cm^{- 1}.

63 Salimbeni A. Paleari F. Canevotti R. Criscuoli M. Lippi A. Angiolini M. Belvisi L. Scolastico C. Colombo L. Bioorg. Med. Chem. Lett.  1997,  7:  2205 

64 Bode W. Mayr I. Baumann U. Huber R. Stone SR. Hofsteenge J. EMBO J.  1989,  8:  3467 

65a Balasubramanian BN. Advances in the Design and Development of Thrombin Inhibitors, Bioorg. Med. Chem.  1995,  3:  999 

65b Tamura SY. Goldman EA. Brunck T. Ripka WC. Semple JE. Bioorg. Med. Chem. Lett.  1997,  7:  331 

65c Balasubramanian N. St. Laurent DR. Federici ME. Meanwell NA. Wright JJ. Schumacher WA. Seiler SM. J. Med. Chem.  1993,  36:  300 

65d Levy OE. Semple JE. Lim ML. Reiner J. Rote WE. Dempsey E. Richard BM. Zhang E. Tulinsky A. Ripka WC. Nutt RF. J. Med. Chem.  1996,  39:  4527 

65e Jackson CV. Wilson HC. Growe VG. Schuman RT. Gesellchen PD. J. Cardiovasc. Pharmacol.  1993,  21:  587 

66 Rick W. Methods of Enzymatic Analysis   Bergmeyer HU. Academic Press; New York: 1963. 

67 Cirillo R. Lippi A. Subissi A. Agnelli G. Criscuoli M. Thromb. Haemostasis  1996,  76:  384 

68a Hanessian S. Sailes H. Munro A. Therrien E. J. Org. Chem.  2003,  68:  7219 

68b Siddiqui MA. Préville P. Tarazi M. Warder SC. Eby P. Gorseth E. Puumala K. DiMaio J. Tetrahedron Lett.  1997,  38:  8807 

69 Ruoslahti E. Pierschbacher MD. Science  1987,  238:  491 

70 Eliceiri BP. Cheresh DAJ. Clin. Invest.  1999,  103:  1227 

71 Ruoslahti E. Ann. Rev. Cell Dev. Biol.  1996,  12:  697 

72a Haubner R. Gratias R. Diefenbach B. Goodman SL. Jonczyk A. Kessler H. J. Am. Chem. Soc.  1996,  118:  7461 

72b Haubner R. Finsinger D. Kessler H. Angew. Chem., Int. Ed. Engl.  1997,  36:  1374 

73a Dechantsreiter MA. Planker E. Mathä B. Lohof E. Hölzemann G. Jonczyk A. Goodman SL. Kessler H. J. Med. Chem.  1999,  42:  3033 

73b Lohof E. Planker E. Mang C. Burkhart F. Dechantsreiter MA. Haubner R. Wester H.-J. Schwaiger M. Hölzemann G. Goodman SL. Kessler H. Angew. Chem. Int. Ed.  2000,  39:  2761 

73c Schumann F. Müller A. Koksch M. Müller G. Sewald N. J. Am. Chem. Soc.  2000,  122:  12009 

73d Haubner R. Schmitt W. Hölzemann G. Goodman SL. Jonczyk A. Kessler H. J. Am. Chem. Soc.  1996,  118:  7881 

74a Belvisi L. Bernardi A. Checchia A. Manzoni L. Potenza D. Scolastico C. Castorina M. Cupelli A. Giannini G. Carminati P. Pisano C. Org. Lett.  2001,  3:  1001 

74b Belvisi L. Caporale A. Colombo M. Manzoni L. Potenza D. Scolastico C. Castorina M. Cati M. Giannini G. Pisano C. Helv. Chim. Acta  2002,  85:  4353 

75 Kumar CC. Nie H. Rogers CP. Malkowski M. Maxwell E. Catino JJ. Armstrong LJ. Pharmacol. Exp. Ther.  1997,  283:  843 

76 Xiong J.-P. Stehle T. Zhang R. Joachimiak A. Frech M. Goodman SL. Arnout MA. Science  2002,  296:  151 

77 Weiner SJ. Kollman PA. Nguyen DT. Case DA. J. Comput. Chem.  1986,  7:  230 

78 Ponder JW. Richards FM. J. Comput. Chem.  1987,  8:  1016 

79 Guarnieri F. Still WC. J. Comput. Chem.  1994,  15:  1302 

80 Gennari C. Gude M. Potenza D. Piarulli U. Chem.-Eur. J.  1998,  4:  1924