ChemComm View Article Online
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
COMMUNICATION
Cite this: Chem. Commun., 2014, 50, 8797 Received 9th May 2014, Accepted 16th June 2014
View Journal | View Issue
Synthesis and structure of oxetane containing tripeptide motifs†‡ Nicola H. Powell,a Guy J. Clarkson,a Rebecca Notman,a Piotr Raubo,b Nathaniel G. Martinb and Michael Shipman*a
DOI: 10.1039/c4cc03507k www.rsc.org/chemcomm
A new class of peptidomimetic is reported in which one of the QO bonds of the peptide backbone is replaced by an amide CQ oxetane ring. They are synthesised by conjugate addition of various a-amino esters to a 3-(nitromethylene)oxetane, reduction of the nitro group and further coupling with N–Z protected amino acids to grow the peptide chain. Structural insights are provided by X-ray diffraction and molecular dynamics simulations.
Peptidomimetics are extremely important in medicinal chemistry offering a number of advantages over physiologically active peptides.1 Consequently, there is an ongoing search for new motifs that effectively mimic the structure and conformation of natural peptides.2 A highly productive approach is to replace one or more of the amide bonds of the backbone with a peptide bond isostere such as an E-alkene, thioamide or sulfonamide.1a,c Since the fourmembered oxetane ring has emerged as an excellent replacement for the carbonyl group in medicinal chemistry,3 we reasoned that substituting one or more of the CQO bonds within the backbone of a peptide with oxetane units could yield an interesting new class of peptidomimetic with greatly reduced vulnerability to proteases (Fig. 1).4 Through the preparation and study of representative peptide-like motifs containing this bioisosteric replacement, we sought to understand how the introduction of a 3-aminooxetane subunit into the peptide backbone modulates its physicochemical properties, conformational preferences and receptor binding. In this communication, we report on the preparation of derivatives in which the central CQO amide bond of a tripeptide
a
Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK. E-mail: [email protected]; Fax: +44 2476 524112; Tel: +44 2476 523186 b AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK † This communication is dedicated to Prof. Richard Taylor on the occasion of his 65th birthday. ‡ Electronic supplementary information (ESI) available: Synthetic procedures and spectroscopic data for 1a–f, 4a–k, 7, chiral HPLC analysis of 4a, X-ray depictions of 1c and 1e, MD simulations for 1e and 8, and the computational methodologies. CCDC 996043 and 996044. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4cc03507k
This journal is © The Royal Society of Chemistry 2014
Fig. 1
Replacement of amide CQO by oxetane ring in peptide chain.
Scheme 1
Synthetic strategy to new oxetane based peptidomimetics.
is replaced by the oxetane nucleus, e.g. 1. The generalised synthetic strategy is given in Scheme 1. It was envisaged that introduction of the 3-aminooxetane subunit might be realised by conjugate addition of chiral a-amino ester 3 to readily accessible oxetane containing nitroalkene 2. Highly nucleophilic primary amines (e.g. BnNH2) are known to undergo rapid conjugate addition to 2 (R = Bn) at room temperature suggesting that this transformation would be facile.3a For general applicability, this interconversion would need to be effective for amino esters derived from a broad spectrum of a-amino acids, and tolerate variation in R within nitroalkene 2. Further chemoselective reduction of the nitro group in 4, and coupling of the resulting amine 5 with an N-protected amino acid would allow the oxetane residue to be positioned centrally within the peptide backbone.
Chem. Commun., 2014, 50, 8797--8800 | 8797
View Article Online
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
Communication
ChemComm
Finally, removal of the C- and N-terminal protecting groups would yield the oxetane based peptidomimetic 1. Importantly, knowledge obtained from making these simple tripeptide motifs would be applicable to the production of larger peptidomimetics through the use of longer peptide fragments as the nucleophile in the conjugate addition step (vide infra); or through further extension of the N-terminus by conventional peptide couplings. Two nitroalkenes 2a (R = H) and 2b (R = Bn) were used in this investigation, to produce peptidomimetics of glycine and phenylalanine respectively (Scheme 2). These were made from commercially available oxetan-3-one (6) and the appropriate nitroalkane by Henry reaction and elimination of the resulting alcohol by way of the mesylate according to published methods.3a,c Conjugate addition of (S)-valine methyl ester (2.0 equiv.) to 2a (1.0 equiv.) provided 4a in 68% yield. In fact, it proved more convenient to generate 2a in situ from 6 (1.0 equiv.) and nitromethane (1.4 equiv.), and react it directly with the (S)-valine methyl ester (2.0 equiv.) without work-up. In this way, 4a was obtained in 65% over the three steps (see ESI‡). Reducing the amount of (S)-valine methyl ester (1.2 equiv.) led to lower yields (40%) and so the amine nucleophile was typically used in 2-fold excess. Using (R)and (S)-4a, made from D- and L-valine methyl ester respectively, it was confirmed by chiral HPLC analysis that no detectable racemization occurs during these conjugate additions (see ESI‡). Similar efficiency was achieved using tetrasubstituted nitroalkene 2b as the acceptor. For example, 4c and 4k were both produced in good yields.§ With respect to the nucleophile, various ester groups
work well. However, the use of benzyl esters was favoured as it allows concomitant deprotection of the N- and C-termini later in the sequence (vide infra). Although our study of amino ester nucleophiles is not exhaustive, success has been achieved with a wide selection of polar and hydrophobic amino acids including Gly (4c,d), Val (4a,b), Thr (4e), Leu (4f), Ile (4g), Phe (4h), and Ser (4i). Moreover, dipeptide based nucleophiles have also been successfully used, enabling the synthesis of 4j and 4k containing longer peptide backbones.¶ The completion of the synthesis of the tripeptide analogues required reduction of the nitro group to enable homologation of the peptide backbone via the corresponding amine. Initially, we tried to isolate these amines but observed the formation of diketopiperazine-like compounds by way of unwanted ring closure. For example, reduction of 4h with Zn–AcOH yielded 7 in 68% after chromatography (Scheme 3). Better results were achieved by immediately coupling the free amine with the appropriate N–Z protected amino acid using EDC–HOBt in EtOH after reduction.5 Excess SmI2 (14 equiv.) in THF–MeOH6 was an effective reducing agent but in some instances unwanted transesterification of the benzyl ester was observed. Indium (4 equiv.) in aq. HCl–THF7 proved more reliable for a range of amines. These amines were immediately coupled using 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC) with representative Cbz-protected amino acids, then the Cbz and benzyl ester groups removed by hydrogenolysis. A selection of representative tripeptide analogues 1a–f were made in high purity and good overall yields using this 3-step sequence (Scheme 3). X-ray diffraction studies performed on single crystals of 1c and 1e grown from methanol unambiguously confirmed their gross structures and provided insights into their conformational
Scheme 2 Conjugate addition of a variety of amino esters and dipeptides to oxetane substituted nitroalkene (2).
Scheme 3 Homologation to tripeptide derivatives 1a–f. 68% yield upon reaction of 4h with Zn–AcOH.
8798 | Chem. Commun., 2014, 50, 8797--8800
a
Produced in
This journal is © The Royal Society of Chemistry 2014
View Article Online
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
ChemComm
Fig. 2 Solid state structure of 1e showing the 4 crystallographically independent molecules in the unit cell, and part of the infinite H-bonded sheet formed by the antiparallel arrangement of the tripeptide chains.
preferences and crystal packing.8 Both these tripeptide mimetics are zwitterionic with the terminal amine, not the central secondary amine, ionised as the ammonium ion. They display antiparallel sheet-like arrangements in the solid state as illustrated for 1e in Fig. 2 (also see ESI‡). Molecular dynamics (MD) simulations were conducted on a representative analogue (1e) and the results compared to those for the parent tripeptide sequence: Leu-Gly-Ile (8). To enable simulations of these molecules, CHARMM-compatible forcefield parameters for the 3-aminooxetane residue were first derived from quantum mechanical calculations (see ESI‡). Each peptide was then simulated for 100 ns in water at 500 K and from this trajectory 10 distinct conformations of each peptide were selected for an additional 100 ns of simulation at 300 K, to yield a total simulation time of 1 ms per peptide. Cluster analysis was performed using 100 000 structures extracted from the trajectories at 10 ps intervals. Eleven distinct structures were found for 1e, compared to seven for 8, indicating that the oxetane based peptidomimetic has greater conformational flexibility. Snapshots of the two most populated clusters for 1e and 8 are presented in Fig. 3 with further analysis provided in the ESI.‡ The conformations explored by the natural peptide are dominated by extended structures where the C and N termini are separated by 47 Å. In contrast, the most populated cluster of 1e is a folded conformation (C to N separation distance of the order of 3–4 Å) that benefits from close contact between the terminal –CO2 and –NH3+ ions. The ability of 1e to more readily accommodate a turn-like feature likely arises from the change in hybridisation and dihedral angle at the central amino oxetane unit.** In summary, we have developed practical methodology for the synthesis of oxetane containing tripeptide motifs, and begun to explore the conformational changes that result from the introduction of the 3-aminooxetane subunit into the peptide backbone. Current work is focused on extending this chemistry to the synthesis and study of larger and more complex derivatives, and
This journal is © The Royal Society of Chemistry 2014
Communication
Fig. 3 Snapshots of the two most populated clusters of 8 and 1e derived from MD simulations, along with the percentages of total structures accounted for by each cluster. Hydrogen atoms omitted for clarity.
to demonstrating the use of oxetane containing peptidomimetics as ligands for biological receptors. We thank EPSRC, the Royal Society and AstraZeneca for financial support. We acknowledge the Centre for Scientific Computing at the University of Warwick for the provision of computing facilities. The Oxford Diffraction Gemini XRD system was obtained, through the Science City Advanced Materials project: Creating and Characterizing Next Generation Advanced Materials.
Notes and references § Phenylalanine analogues 4c and 4k were produced as racemates. Addition of chiral amino esters to 2b such as (S)-valine methyl ester proceeded in high yield but low diastereoselectivity (d.r. = 45 : 55). ¶ Amino ester nucleophile = (S)-H2NCH(iPr)C(QO)NHCH2CO2Bn for 4j; amino ester = H2NCH2C(QO)NHCH2CO2Bn for 4k. 8 CCDC 996044 crystal data: 1c, C19H29N3O4, 0.1 (CH4O) (M = 366.65): triclinic, space group P1 (no. 1), a = 8.4127(4) Å, b = 9.5002(5) Å, c = 13.3202(8) Å, a = 96.096(5)1, b = 104.312(5)1, g = 90.121(4)1, V = 1025.27(10) Å3, Z = 2, T = 150(2) K, m(CuKa) = 0.683 mm 1, Dcalc = 1.188 g mm 3, 19 052 reflections measured (6.89 r 2Y r 158.46), 8088 unique (Rint = 0.0470, Rsigma = 0.0526) which were used in all calculations. The final R1 was 0.0506 (I 4 2s(I)) and wR2 was 0.1426 (all data). CCDC 996043 crystal data: 1e, C16H31N3O4 (M = 329.44): triclinic, space group P1 (no. 1), a = 8.5557(2) Å, b = 14.0932(5) Å, c = 16.3070(4) Å, a = 77.134(3)1, b = 81.935(2)1, g = 80.958(2)1, V = 1881.70(9) Å3, Z = 4, T = 150(2) K, m(CuKa) = 0.679 mm 1, Dcalc = 1.163 g mm 3, 34 050 reflections measured (6.488 r 2Y r 156.87), 14 895 unique (Rint = 0.0468, Rsigma = 0.0504) which were used in all calculations. The final R1 was 0.0646 (I 4 2s(I)) and wR2 was 0.1839 (all data). ** From the X-ray crystal structure of 1e, the nitrogen atom adjacent to the oxetane is pyramidal and the averaged C–N–Cox–C torsional angle, o = 60.21 (cf. o E 1801 in a conventional sp2-hybridised peptide bond). 1 For reviews, see: (a) R. M. J. Liskamp, D. T. S. Rijkers, J. A. W. Kruijtzer and J. Kemmink, ChemBioChem, 2011, 12, 1626–1653; (b) P. G. Vasudev, S. Chatterjee, N. Shamala and P. Balaram, Chem. Rev., 2011, 111, 657–687; (c) J. Vagner, H. Qu and V. J. Hruby, Curr. Opin. Chem. Biol., 2008, 12, 292–296; (d) D. Seebach and J. Gardiner, Acc. Chem. Res., 2008, 41, 1366–1375; (e) A. S. Ripka and D. H. Rich, Curr. Opin. Chem. Biol., 1998, 2, 441–452; ( f ) J. Gante, Angew. Chem., Int. Ed. Engl., 1994, 33, 1699–1720;
Chem. Commun., 2014, 50, 8797--8800 | 8799
View Article Online
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
Communication (g) A. Giannis and T. Kolter, Angew. Chem., Int. Ed. Engl., 1993, 32, 1244–1267. 2 For recent illustrative examples, see: (a) I. E. Valverde, A. Bauman, C. A. Kluba, S. Vomstein, M. A. Walter and T. L. Mindt, Angew. Chem., Int. Ed., 2013, 52, 8957–8960; (b) T. Kawakami, T. Ishizawa and H. Murakami, J. Am. Chem. Soc., 2013, 135, 12297–12304; (c) A. Brust, C.-I. A. Wang, N. L. Daly, J. Kennerly, M. Sadeghi, M. J. Christie, R. J. Lewis, M. Mobli and P. F. Alewood, Angew. Chem., Int. Ed., 2013, 52, 12020–12023; (d) G. K. S. Prakash, C. Ni, F. Wang, Z. Zhang, R. Haiges and G. A. Olah, Angew. Chem., Int. Ed., 2013, 52, 10835–10839; (e) N. Pendem, C. Douat, P. Claudon, M. Laguerre, S. Castano, B. Desbat, D. Cavagnat, E. Ennifar, B. Kauffmann and G. Guichard, J. Am. Chem. Soc., 2013, 135, 4884–4892; ( f ) A. G. Jamieson, D. Russell and A. D. Hamilton, Chem. Commun., 2012, 48, 3709–3711; (g) C. L. Sutherell, S. Thompson, R. T. W. Scott and A. D. Hamilton, Chem. Commun., 2012, 48, 9834–9836; (h) I. E. Andersson, T. Batsalova, S. Haag, B. Dzhambazov, R. Holmdahl, J. Kihlberg and A. Linusson, J. Am. Chem. Soc., 2011, 133, 14368–14378; (i) E. Ko, J. Liu, L. M. Perez, G. Lu, A. Schaefer and K. Burgess, J. Am. Chem. Soc., 2011, 133, 462–477; ( j) H. N. Hoang, R. W. Driver, R. L. Beyer, A. K. Malde, G. T. Le, G. Abbenante, A. E. Mark and D. P. Fairlie, Angew. Chem., Int. Ed., 2011, 50, 11107–11111.
8800 | Chem. Commun., 2014, 50, 8797--8800
ChemComm 3 (a) J. A. Burkhard, B. H. Tchitchanov and E. M. Carreira, Angew. Chem., Int. Ed., 2011, 50, 5379–5382; (b) G. Wuitschik, E. M. Carreira, B. Wagner, ¨ller, J. Med. H. Fischer, I. Parrilla, F. Schuler, M. Rogers-Evans and K. Mu ¨ller, Chem., 2010, 53, 3227–3246; (c) G. Wuitschik, M. Rogers-Evans, K. Mu H. Fischer, B. Wagner, F. Schuler, L. Polonchuk and E. M. Carreira, Angew. Chem., Int. Ed., 2006, 45, 7736–7739. 4 Foldamers containing oxetane subunits have been described, see (a) T. D. W. Claridge, J. M. Goodman, A. Moreno, D. Angus, S. F. Barker, C. Taillefumier, M. P. Watterson and G. W. J. Fleet, Tetrahedron Lett., 2001, 42, 4251–4255; (b) T. D. W. Claridge, B. LopezOrtega, S. F. Jenkinson and G. W. J. Fleet, Tetrahedron: Asymmetry, 2008, 19, 984–988; (c) S. D. Lucas, A. P. Rauter, J. Schneider and H. P. Wessel, J. Carbohydr. Chem., 2009, 28, 431–446; (d) S. D. Lucas, H. Fischer, A. Alker, A. P. Rauter and H. P. Wessel, J. Carbohydr. Chem., 2011, 30, 498–548. 5 Y. J. Pu, R. K. Vaid, S. K. Boini, R. W. Towsley, C. W. Doecke and D. Mitchell, Org. Process Res. Dev., 2009, 13, 310–314. 6 B. Ma, B. Banerjee, D. N. Litvinov, L. He and S. L. Castle, J. Am. Chem. Soc., 2010, 132, 1159–1171. 7 V. Singh, S. Kanojiyab and S. Batra, Tetrahedron, 2006, 62, 10100–10110.
This journal is © The Royal Society of Chemistry 2014
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
COMMUNICATION
Cite this: Chem. Commun., 2014, 50, 8797 Received 9th May 2014, Accepted 16th June 2014
View Journal | View Issue
Synthesis and structure of oxetane containing tripeptide motifs†‡ Nicola H. Powell,a Guy J. Clarkson,a Rebecca Notman,a Piotr Raubo,b Nathaniel G. Martinb and Michael Shipman*a
DOI: 10.1039/c4cc03507k www.rsc.org/chemcomm
A new class of peptidomimetic is reported in which one of the QO bonds of the peptide backbone is replaced by an amide CQ oxetane ring. They are synthesised by conjugate addition of various a-amino esters to a 3-(nitromethylene)oxetane, reduction of the nitro group and further coupling with N–Z protected amino acids to grow the peptide chain. Structural insights are provided by X-ray diffraction and molecular dynamics simulations.
Peptidomimetics are extremely important in medicinal chemistry offering a number of advantages over physiologically active peptides.1 Consequently, there is an ongoing search for new motifs that effectively mimic the structure and conformation of natural peptides.2 A highly productive approach is to replace one or more of the amide bonds of the backbone with a peptide bond isostere such as an E-alkene, thioamide or sulfonamide.1a,c Since the fourmembered oxetane ring has emerged as an excellent replacement for the carbonyl group in medicinal chemistry,3 we reasoned that substituting one or more of the CQO bonds within the backbone of a peptide with oxetane units could yield an interesting new class of peptidomimetic with greatly reduced vulnerability to proteases (Fig. 1).4 Through the preparation and study of representative peptide-like motifs containing this bioisosteric replacement, we sought to understand how the introduction of a 3-aminooxetane subunit into the peptide backbone modulates its physicochemical properties, conformational preferences and receptor binding. In this communication, we report on the preparation of derivatives in which the central CQO amide bond of a tripeptide
a
Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK. E-mail: [email protected]; Fax: +44 2476 524112; Tel: +44 2476 523186 b AstraZeneca, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK † This communication is dedicated to Prof. Richard Taylor on the occasion of his 65th birthday. ‡ Electronic supplementary information (ESI) available: Synthetic procedures and spectroscopic data for 1a–f, 4a–k, 7, chiral HPLC analysis of 4a, X-ray depictions of 1c and 1e, MD simulations for 1e and 8, and the computational methodologies. CCDC 996043 and 996044. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4cc03507k
This journal is © The Royal Society of Chemistry 2014
Fig. 1
Replacement of amide CQO by oxetane ring in peptide chain.
Scheme 1
Synthetic strategy to new oxetane based peptidomimetics.
is replaced by the oxetane nucleus, e.g. 1. The generalised synthetic strategy is given in Scheme 1. It was envisaged that introduction of the 3-aminooxetane subunit might be realised by conjugate addition of chiral a-amino ester 3 to readily accessible oxetane containing nitroalkene 2. Highly nucleophilic primary amines (e.g. BnNH2) are known to undergo rapid conjugate addition to 2 (R = Bn) at room temperature suggesting that this transformation would be facile.3a For general applicability, this interconversion would need to be effective for amino esters derived from a broad spectrum of a-amino acids, and tolerate variation in R within nitroalkene 2. Further chemoselective reduction of the nitro group in 4, and coupling of the resulting amine 5 with an N-protected amino acid would allow the oxetane residue to be positioned centrally within the peptide backbone.
Chem. Commun., 2014, 50, 8797--8800 | 8797
View Article Online
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
Communication
ChemComm
Finally, removal of the C- and N-terminal protecting groups would yield the oxetane based peptidomimetic 1. Importantly, knowledge obtained from making these simple tripeptide motifs would be applicable to the production of larger peptidomimetics through the use of longer peptide fragments as the nucleophile in the conjugate addition step (vide infra); or through further extension of the N-terminus by conventional peptide couplings. Two nitroalkenes 2a (R = H) and 2b (R = Bn) were used in this investigation, to produce peptidomimetics of glycine and phenylalanine respectively (Scheme 2). These were made from commercially available oxetan-3-one (6) and the appropriate nitroalkane by Henry reaction and elimination of the resulting alcohol by way of the mesylate according to published methods.3a,c Conjugate addition of (S)-valine methyl ester (2.0 equiv.) to 2a (1.0 equiv.) provided 4a in 68% yield. In fact, it proved more convenient to generate 2a in situ from 6 (1.0 equiv.) and nitromethane (1.4 equiv.), and react it directly with the (S)-valine methyl ester (2.0 equiv.) without work-up. In this way, 4a was obtained in 65% over the three steps (see ESI‡). Reducing the amount of (S)-valine methyl ester (1.2 equiv.) led to lower yields (40%) and so the amine nucleophile was typically used in 2-fold excess. Using (R)and (S)-4a, made from D- and L-valine methyl ester respectively, it was confirmed by chiral HPLC analysis that no detectable racemization occurs during these conjugate additions (see ESI‡). Similar efficiency was achieved using tetrasubstituted nitroalkene 2b as the acceptor. For example, 4c and 4k were both produced in good yields.§ With respect to the nucleophile, various ester groups
work well. However, the use of benzyl esters was favoured as it allows concomitant deprotection of the N- and C-termini later in the sequence (vide infra). Although our study of amino ester nucleophiles is not exhaustive, success has been achieved with a wide selection of polar and hydrophobic amino acids including Gly (4c,d), Val (4a,b), Thr (4e), Leu (4f), Ile (4g), Phe (4h), and Ser (4i). Moreover, dipeptide based nucleophiles have also been successfully used, enabling the synthesis of 4j and 4k containing longer peptide backbones.¶ The completion of the synthesis of the tripeptide analogues required reduction of the nitro group to enable homologation of the peptide backbone via the corresponding amine. Initially, we tried to isolate these amines but observed the formation of diketopiperazine-like compounds by way of unwanted ring closure. For example, reduction of 4h with Zn–AcOH yielded 7 in 68% after chromatography (Scheme 3). Better results were achieved by immediately coupling the free amine with the appropriate N–Z protected amino acid using EDC–HOBt in EtOH after reduction.5 Excess SmI2 (14 equiv.) in THF–MeOH6 was an effective reducing agent but in some instances unwanted transesterification of the benzyl ester was observed. Indium (4 equiv.) in aq. HCl–THF7 proved more reliable for a range of amines. These amines were immediately coupled using 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC) with representative Cbz-protected amino acids, then the Cbz and benzyl ester groups removed by hydrogenolysis. A selection of representative tripeptide analogues 1a–f were made in high purity and good overall yields using this 3-step sequence (Scheme 3). X-ray diffraction studies performed on single crystals of 1c and 1e grown from methanol unambiguously confirmed their gross structures and provided insights into their conformational
Scheme 2 Conjugate addition of a variety of amino esters and dipeptides to oxetane substituted nitroalkene (2).
Scheme 3 Homologation to tripeptide derivatives 1a–f. 68% yield upon reaction of 4h with Zn–AcOH.
8798 | Chem. Commun., 2014, 50, 8797--8800
a
Produced in
This journal is © The Royal Society of Chemistry 2014
View Article Online
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
ChemComm
Fig. 2 Solid state structure of 1e showing the 4 crystallographically independent molecules in the unit cell, and part of the infinite H-bonded sheet formed by the antiparallel arrangement of the tripeptide chains.
preferences and crystal packing.8 Both these tripeptide mimetics are zwitterionic with the terminal amine, not the central secondary amine, ionised as the ammonium ion. They display antiparallel sheet-like arrangements in the solid state as illustrated for 1e in Fig. 2 (also see ESI‡). Molecular dynamics (MD) simulations were conducted on a representative analogue (1e) and the results compared to those for the parent tripeptide sequence: Leu-Gly-Ile (8). To enable simulations of these molecules, CHARMM-compatible forcefield parameters for the 3-aminooxetane residue were first derived from quantum mechanical calculations (see ESI‡). Each peptide was then simulated for 100 ns in water at 500 K and from this trajectory 10 distinct conformations of each peptide were selected for an additional 100 ns of simulation at 300 K, to yield a total simulation time of 1 ms per peptide. Cluster analysis was performed using 100 000 structures extracted from the trajectories at 10 ps intervals. Eleven distinct structures were found for 1e, compared to seven for 8, indicating that the oxetane based peptidomimetic has greater conformational flexibility. Snapshots of the two most populated clusters for 1e and 8 are presented in Fig. 3 with further analysis provided in the ESI.‡ The conformations explored by the natural peptide are dominated by extended structures where the C and N termini are separated by 47 Å. In contrast, the most populated cluster of 1e is a folded conformation (C to N separation distance of the order of 3–4 Å) that benefits from close contact between the terminal –CO2 and –NH3+ ions. The ability of 1e to more readily accommodate a turn-like feature likely arises from the change in hybridisation and dihedral angle at the central amino oxetane unit.** In summary, we have developed practical methodology for the synthesis of oxetane containing tripeptide motifs, and begun to explore the conformational changes that result from the introduction of the 3-aminooxetane subunit into the peptide backbone. Current work is focused on extending this chemistry to the synthesis and study of larger and more complex derivatives, and
This journal is © The Royal Society of Chemistry 2014
Communication
Fig. 3 Snapshots of the two most populated clusters of 8 and 1e derived from MD simulations, along with the percentages of total structures accounted for by each cluster. Hydrogen atoms omitted for clarity.
to demonstrating the use of oxetane containing peptidomimetics as ligands for biological receptors. We thank EPSRC, the Royal Society and AstraZeneca for financial support. We acknowledge the Centre for Scientific Computing at the University of Warwick for the provision of computing facilities. The Oxford Diffraction Gemini XRD system was obtained, through the Science City Advanced Materials project: Creating and Characterizing Next Generation Advanced Materials.
Notes and references § Phenylalanine analogues 4c and 4k were produced as racemates. Addition of chiral amino esters to 2b such as (S)-valine methyl ester proceeded in high yield but low diastereoselectivity (d.r. = 45 : 55). ¶ Amino ester nucleophile = (S)-H2NCH(iPr)C(QO)NHCH2CO2Bn for 4j; amino ester = H2NCH2C(QO)NHCH2CO2Bn for 4k. 8 CCDC 996044 crystal data: 1c, C19H29N3O4, 0.1 (CH4O) (M = 366.65): triclinic, space group P1 (no. 1), a = 8.4127(4) Å, b = 9.5002(5) Å, c = 13.3202(8) Å, a = 96.096(5)1, b = 104.312(5)1, g = 90.121(4)1, V = 1025.27(10) Å3, Z = 2, T = 150(2) K, m(CuKa) = 0.683 mm 1, Dcalc = 1.188 g mm 3, 19 052 reflections measured (6.89 r 2Y r 158.46), 8088 unique (Rint = 0.0470, Rsigma = 0.0526) which were used in all calculations. The final R1 was 0.0506 (I 4 2s(I)) and wR2 was 0.1426 (all data). CCDC 996043 crystal data: 1e, C16H31N3O4 (M = 329.44): triclinic, space group P1 (no. 1), a = 8.5557(2) Å, b = 14.0932(5) Å, c = 16.3070(4) Å, a = 77.134(3)1, b = 81.935(2)1, g = 80.958(2)1, V = 1881.70(9) Å3, Z = 4, T = 150(2) K, m(CuKa) = 0.679 mm 1, Dcalc = 1.163 g mm 3, 34 050 reflections measured (6.488 r 2Y r 156.87), 14 895 unique (Rint = 0.0468, Rsigma = 0.0504) which were used in all calculations. The final R1 was 0.0646 (I 4 2s(I)) and wR2 was 0.1839 (all data). ** From the X-ray crystal structure of 1e, the nitrogen atom adjacent to the oxetane is pyramidal and the averaged C–N–Cox–C torsional angle, o = 60.21 (cf. o E 1801 in a conventional sp2-hybridised peptide bond). 1 For reviews, see: (a) R. M. J. Liskamp, D. T. S. Rijkers, J. A. W. Kruijtzer and J. Kemmink, ChemBioChem, 2011, 12, 1626–1653; (b) P. G. Vasudev, S. Chatterjee, N. Shamala and P. Balaram, Chem. Rev., 2011, 111, 657–687; (c) J. Vagner, H. Qu and V. J. Hruby, Curr. Opin. Chem. Biol., 2008, 12, 292–296; (d) D. Seebach and J. Gardiner, Acc. Chem. Res., 2008, 41, 1366–1375; (e) A. S. Ripka and D. H. Rich, Curr. Opin. Chem. Biol., 1998, 2, 441–452; ( f ) J. Gante, Angew. Chem., Int. Ed. Engl., 1994, 33, 1699–1720;
Chem. Commun., 2014, 50, 8797--8800 | 8799
View Article Online
Published on 17 June 2014. Downloaded by University of Michigan Library on 21/10/2014 20:58:27.
Communication (g) A. Giannis and T. Kolter, Angew. Chem., Int. Ed. Engl., 1993, 32, 1244–1267. 2 For recent illustrative examples, see: (a) I. E. Valverde, A. Bauman, C. A. Kluba, S. Vomstein, M. A. Walter and T. L. Mindt, Angew. Chem., Int. Ed., 2013, 52, 8957–8960; (b) T. Kawakami, T. Ishizawa and H. Murakami, J. Am. Chem. Soc., 2013, 135, 12297–12304; (c) A. Brust, C.-I. A. Wang, N. L. Daly, J. Kennerly, M. Sadeghi, M. J. Christie, R. J. Lewis, M. Mobli and P. F. Alewood, Angew. Chem., Int. Ed., 2013, 52, 12020–12023; (d) G. K. S. Prakash, C. Ni, F. Wang, Z. Zhang, R. Haiges and G. A. Olah, Angew. Chem., Int. Ed., 2013, 52, 10835–10839; (e) N. Pendem, C. Douat, P. Claudon, M. Laguerre, S. Castano, B. Desbat, D. Cavagnat, E. Ennifar, B. Kauffmann and G. Guichard, J. Am. Chem. Soc., 2013, 135, 4884–4892; ( f ) A. G. Jamieson, D. Russell and A. D. Hamilton, Chem. Commun., 2012, 48, 3709–3711; (g) C. L. Sutherell, S. Thompson, R. T. W. Scott and A. D. Hamilton, Chem. Commun., 2012, 48, 9834–9836; (h) I. E. Andersson, T. Batsalova, S. Haag, B. Dzhambazov, R. Holmdahl, J. Kihlberg and A. Linusson, J. Am. Chem. Soc., 2011, 133, 14368–14378; (i) E. Ko, J. Liu, L. M. Perez, G. Lu, A. Schaefer and K. Burgess, J. Am. Chem. Soc., 2011, 133, 462–477; ( j) H. N. Hoang, R. W. Driver, R. L. Beyer, A. K. Malde, G. T. Le, G. Abbenante, A. E. Mark and D. P. Fairlie, Angew. Chem., Int. Ed., 2011, 50, 11107–11111.
8800 | Chem. Commun., 2014, 50, 8797--8800
ChemComm 3 (a) J. A. Burkhard, B. H. Tchitchanov and E. M. Carreira, Angew. Chem., Int. Ed., 2011, 50, 5379–5382; (b) G. Wuitschik, E. M. Carreira, B. Wagner, ¨ller, J. Med. H. Fischer, I. Parrilla, F. Schuler, M. Rogers-Evans and K. Mu ¨ller, Chem., 2010, 53, 3227–3246; (c) G. Wuitschik, M. Rogers-Evans, K. Mu H. Fischer, B. Wagner, F. Schuler, L. Polonchuk and E. M. Carreira, Angew. Chem., Int. Ed., 2006, 45, 7736–7739. 4 Foldamers containing oxetane subunits have been described, see (a) T. D. W. Claridge, J. M. Goodman, A. Moreno, D. Angus, S. F. Barker, C. Taillefumier, M. P. Watterson and G. W. J. Fleet, Tetrahedron Lett., 2001, 42, 4251–4255; (b) T. D. W. Claridge, B. LopezOrtega, S. F. Jenkinson and G. W. J. Fleet, Tetrahedron: Asymmetry, 2008, 19, 984–988; (c) S. D. Lucas, A. P. Rauter, J. Schneider and H. P. Wessel, J. Carbohydr. Chem., 2009, 28, 431–446; (d) S. D. Lucas, H. Fischer, A. Alker, A. P. Rauter and H. P. Wessel, J. Carbohydr. Chem., 2011, 30, 498–548. 5 Y. J. Pu, R. K. Vaid, S. K. Boini, R. W. Towsley, C. W. Doecke and D. Mitchell, Org. Process Res. Dev., 2009, 13, 310–314. 6 B. Ma, B. Banerjee, D. N. Litvinov, L. He and S. L. Castle, J. Am. Chem. Soc., 2010, 132, 1159–1171. 7 V. Singh, S. Kanojiyab and S. Batra, Tetrahedron, 2006, 62, 10100–10110.
This journal is © The Royal Society of Chemistry 2014
