The synthesis and crystal structure of Cbz-[(1R,2S)-ACPC]3-OH: A tripeptide derived from the β-amino acid (1R,2S)-cispentacin

Article abstract of DOI:10.1007/s10870-014-0502-x

Crystals of the tripeptide Cbz-[(1R,2S)-ACPC]₃-OH 4, derived from the β-amino acid (1R,2S)-2-aminocyclopentanecarboxylic acid, were synthesised and studied by X-ray diffraction. Tripeptide 4 crystallizes in the orthorhombic space group P 2 ₁ 2 ₁ 2 ₁ with cell parameters of a = 7.8957(1) A, b = 12.9289(2) A, c = 24.7850(4) A, V = 2530.12(6) A³ and Z = 4. Adjacent molecules are linked by a series of N-H···O=C and O- H···O=C hydrogen bonds to form a double tape-like arrangement. Graphical Abstract: The structure of a tripeptide derived from the β-amino acid (1R,2S)-2-aminocyclopentanecarboxylic acid has been analysed by X-ray diffraction.[Figure not available: see fulltext.]

Full text of DOI:10.1007/s10870-014-0502-x

J Chem Crystallogr (2014) 44:205–209
DOI 10.1007/s10870-014-0502-x
ORIGINAL PAPER
The Synthesis and Crystal Structure of Cbz-[(1R,2S)-ACPC]3-OH:
A Tripeptide Derived from the b-Amino Acid (1R,2S)-Cispentacin
•
•
•
Stephen G. Davies Elin Siddall Amber L. Thompson
James E. Thomson
Received: 17 December 2013 / Accepted: 26 February 2014 / Published online: 12 March 2014
Ó Springer Science+Business Media New York 2014
Abstract Crystals of the tripeptide Cbz-[(1R,2S)-
ACPC]3-OH 4, derived from the b-amino acid (1R,2S)-2-
aminocyclopentanecarboxylic acid, were synthesised and
studied by X-ray diffraction. Tripeptide 4 crystallizes in the
orthorhombic space group P 212121 with cell parameters of
derived from (1R,2S)-ACPC, forms a non-polar strand and
adopts a sheet-like structure in solution [32]. We have also
reported crystallographic analyses of dimers 1 and 2
(Fig. 1), derived from (1R,2S)-ACPC and (1S,2R,3S)-3-
Me-ACPC, respectively, which form b-sheet like structures
in the solid state resulting from arrays of N–HÁÁÁO=C
hydrogen bonds [33]. Herein we report the synthesis and
crystal structure of Cbz-[(1R,2S)-ACPC]3-OH 4, a tripep-
tide derived from (1R,2S)-ACPC.
˚
a = 7.8957(1) A, b = 12.9289(2) A, c = 24.7850(4) A,
˚
˚
3
V = 2530.12(6) A and Z = 4. Adjacent molecules are
˚
linked by a series of N–HÁÁÁO=C and O–HÁÁÁO=C hydrogen
bonds to form a double tape-like arrangement.
Keywords b-Peptide Á b-Sheet Á Cispentacin
Experimental
Introduction
Synthesis
b-Peptides [1–19] are known to offer improved bioavail-
ability and therapeutic lifetimes when compared to their
a-amino acid derived analogues [20–24], whilst still dis-
playing potent biological activity [25–27]. As such, there
has been intense interest in the secondary structural char-
acteristics of oligomers of the cyclic b-amino acids ci-
spentacin and transpentacin, the diastereoisomers of
2-aminocyclopentanecarboxylic acid (ACPC) [28–31]. For
All reagents were used as supplied without prior purifica-
tion. Elemental analyses were recorded by the microanal-
ysis service of the London Metropolitan University, UK.
Melting points were recorded on a Gallenkamp Hot Stage
apparatus and are uncorrected. IR spectra were recorded on
a Bruker Tensor 27 FT-IR spectrometer as KBr discs.
Selected characteristic peaks are reported in cm-1. NMR
spectra were recorded on Bruker Avance spectrometers in
the deuterated solvent stated. Spectra were recorded at rt.
The field was locked by external referencing to the relevant
deuteron resonance. Low-resolution mass spectra were
recorded on either a VG MassLab 20–250 or a Micromass
Platform 1 spectrometer. Accurate mass measurements
were run on a Micromass GCT instrument fitted with a
Scientific Glass Instruments BPX5 column (15 m 9
0.25 mm) using amyl acetate as a lock mass. In each case,
product distributions and diastereoisomeric ratios were
determined by integration of the 400 MHz 1H NMR
spectra of the crude reaction mixtures and isolated
products.
¨
example, Fu¨lop et al. have reported that pentamer 3,
S. G. Davies (&) Á E. Siddall Á A. L. Thompson Á
J. E. Thomson
Department of Chemistry, Chemistry Research Laboratory,
University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
e-mail: steve.davies@chem.ox.ac.uk
123

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J Chem Crystallogr (2014) 44:205–209
(368 mg, 1.40 mmol, [99:1 dr) [34] and EDCÁHCl
(322 mg, 1.68 mmol) under anhydrous conditions. After
16 h, the reaction mixture was washed with 1.0 M aq HCl
(20 mL), satd aq NaHCO3 (20 mL) and brine (20 mL),
then dried over MgSO4 and concentrated in vacuo. Purifi-
cation via recrystallisation (CHCl3/heptane) gave 7 as a
white solid (443 mg, 58 %, [99:1 dr); C30H43N3O6
requires C, 66.5; H, 8.0; N, 7.8 %; found C, 66.5; H, 8.1;
N, 7.7 %; mp 144–146 °C (CHCl3/heptane); [a]2D3–85.0
(c 1.0 in CHCl3); vmax (KBr) 3327 (N–H), 1714, 1694,
1650, 1542 (C=O); dH (400 MHz, CDCl3) 1.37–2.02 (18H,
m, 3 9 C(3)H2, 3 9 C(4)H2, 3 9 C(5)H2), 1.43 (9H, s,
CMe3), 2.67 (1H, obsc m, C(1)H), 2.73 (1H, obsc m,
C(1)H), 2.80–2.90 (1H, m, C(1)H), 4.17 (1H, app t, J 7.5,
C(2)H), 4.38 (1H, obsc m, C(2)H), 4.41 (1H, obsc m,
C(2)H), 5.04 (1H, d, J 12.3, CHAHBPh), 5.10 (1H, d,
J 12.3, CHAHBPh), 5.50 (1H, d, J 7.9, NH), 6.26 (1H, d,
J 8.5, NH), 6.43 (1H, d, J 7.9, NH), 7.26–7.40 (5H, m, Ph);
dC (100 MHz, CDCl3) 22.2, 22.7, 22.8, 28.1, 28.3, 28.7,
32.4, 32.8, 32.9 (3 9 C(3), 3 9 C(4), 3 9 C(5)), 28.1
(CMe3), 47.3, 47.7, 47.7 (3 9 C(1)), 52.0, 52.5, 54.5
(3 9 C(2)), 66.5 (CH2Ph), 80.9 (CMe3), 128.0, 128.4
(o,m,p-Ph), 136.6 (i-Ph), 156.1 (NCO, carbamate), 173.2,
173.3, 173.7 (2 9 NCO, amide; COt2Bu); m/z (ESI?) 542
Fig. 1 Dimer 1, trimer 4 and pentamer 3 [derived from (1R,2S)-
ACPC] and dimer 2 [derived from (1S,2R,3S)-3-Me-ACPC]
H-[(1R,2S)-ACPC]2-OtBu 6
([M?H]?, 100 %); HRMS (ESI?) C30H43N3NaO6
?
([M?Na]?) requires 564.3044; found 564.3045.
Pd(OH)2/C (25 % by wt, 488 mg) was added to a stirred,
degassed solution of 5 (1.95 g, 4.50 mmol, [99:1 dr) [33]
in MeOH/AcOH (40:1 mL). The resultant suspension was
stirred under H2 (1 atm) for 16 h. The reaction mixture was
then filtered through CeliteÒ (eluent MeOH) and concen-
trated in vacuo. The residue was dissolved in CH2Cl2
(50 mL) and the resultant solution was washed with satd aq
NaHCO3 (3 9 50 mL) and brine (50 mL), then dried over
MgSO4 and concentrated in vacuo to give 6 as a white solid
(1.24 g, 92 %, [99:1 dr); mp 74 °C; [a]2D2–42.7 (c 1.0 in
CHCl3); vmax (KBr) 3319 (br, N–H), 1699 (br, C=O); dH
(400 MHz, CDCl3) 1.44 (9H, s, CMe3), 1.46–2.03 (14H, m,
2 9 C(3)H2, 2 9 C(4)H2, 2 9 C(5)H2, NH2), 2.45–2.54
(1H, m, C(1)H), 2.83–2.91 (1H, m, C(1)H), 3.46–3.56 (1H,
m, C(2)H), 4.47–4.56 (1H, m, C(2)H), 7.05 (1H, d, J 7.2
NH); dC (100 MHz, CDCl3) 22.1, 22.2, 26.8, 28.0, 32.5,
35.1 (2 9 C(3), 2 9 C(4), 2 9 C(5)), 28.1 (CMe3), 47.5,
50.9 (2 9 C(1)), 51.9, 54.7 (2 9 C(2)), 80.7 (CMe3),
173.2, 174.0 (NCO, COt2Bu); m/z (ESI?) 297 ([M?H]?,
Cbz-[(1R,2S)-ACPC]3-OH 4
TFA (0.70 mL) was added to a stirred solution of 7
(250 mg, 0.46 mmol, [99:1 dr) in CH2Cl2 (2.10 mL) at
0 °C. The resultant mixture was allowed to warm to rt and
stirred for 3 h before being concentrated in vacuo and dried
under high vacuum. Purification via recrystallisation
(CHCl3/heptane) gave 4 as a white solid (157 mg, 70 %,
[99:1 dr); mp 170–172 °C (CHCl3/heptane); [a]2D0–101.7
(c 0.6 in MeOH); vmax (KBr) 3340 (br, N–H, O–H),
1701, 1662, 1542 (C=O); dH (400 MHz, CDCl3,
26 mM) 1.39–2.11 (18H, m, 3 9 C(3)H2, 3 9 C(4)H2,
3 9 C(5)H2), 2.70–2.90 (2H, m, 2 9 C(1)H), 2.98–3.10
(1H, m, C(1)H), 4.22 (1H, obsc m, C(2)H), 4.33 (1H, obsc
m, C(2)H), 4.46 (1H, obsc m, C(2)H), 5.04 (1H, d, J 12.4,
CHAHBPh), 5.11 (1H, d, J 12.4, CHAHBPh), 5.42 (1H, d,
J 8.6, NH), 6.61 (1H, d, J 8.1, NH), 6.89 (1H, d, J 8.3, NH),
7.22–7.39 (5H, m, Ph); dC (100 MHz, MeOH-d4) 22.2,
22.9, 27.9, 28.2, 28.5, 31.6, 32.4, 32.9 (3 9 C(3),
3 9 C(4), 3 9 C(5)), 46.1, 47.7, 47.8 (3 9 C(1)), 52.0,
52.7, 54.6 (3 9 C(2)), 66.7 (CH2Ph), 128.0, 128.1, 128.5
(o,m,p-Ph), 136.4 (i-Ph), 156.2 (NCO, carbamate), 173.6,
173.9, 176.8 (2 9 NCO, amide; CO2H); m/z (ESI?) 508
100 %); HRMS (ESI?) C16H29N2O3 ([M?H]?) requires
?
297.2173; found 297.2173.
Cbz-[(1R,2S)-ACPC]3-OtBu 7
A stirred solution of 6 (415 mg, 1.40 mmol, [99:1 dr) in
CHCl3 (10 mL) was successively treated with Et3N
(1.00 mL, 7.00 mmol), HOBt (227 mg, 1.68 mmol), 8
([M?Na]?, 100 %); HRMS (ESI?) C26H36N3O6
([M?H]?) requires 486.2599; found 486.2598.
?
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J Chem Crystallogr (2014) 44:205–209
207
Table 1 Crystallographic data and refinement details for tripeptide 4
Compound
4
Empirical formula
Formula weight
Crystal habit, colour
Crystal system
C26H35N3O6
485.58
Plate, colourless
Orthorhombic
Space group
P212121
˚
a (A)
7.8957(1)
˚
b (A)
12.9289(2)
˚
c (A)
24.7850(4)
a (°)
b (°)
c (°)
90
90
90
3
˚
Volume (A )
2530.12(6)
Z
4
Density (calc. g cm-3
Temperature (K)
)
1.275
190
˚
Radiation type/k (A)
Mo Ka/0.71073
Absorption coeff. (mm-1
)
0.091
Scheme 1 Reagents and conditions: (i) Pd(OH)2/C, H2 (1 atm),
MeOH/AcOH (40:1), 16 h; (ii) 8, EDCÁHCl, HOBt, NEt3, CHCl3, rt,
16 h; (iii) TFA/CH2Cl2 (1:3), 0 °C to rt, 3 h
F(000)
1,040
Crystal size (mm)
Reflections measured
Independent reflections
0.05 9 0.20 9 0.20
5,776
3,277
Selected structural details for tripeptide 4 are included in
Table 1 and full crystallographic data have been deposited
with the Cambridge Crystallographic Data Centre as sup-
plementary publication number CCDC 977339. Copies of
these data can be obtained free of charge from The Cam-
bridge Crystallographic Data Centre via www.ccdc.cam.ac.
uk/data_request/cif.
Observed reflns. [I [ 2.0r(I)]
Number of parameters
Goodness-of-fit on F2
2,139
316
0.9978
Final R indices [I [ 2.0r(I)]
R indices [all data]
-3
R1 = 0.042, wR2 = 0.094
R1 = 0.073, wR2 = 0.103
0.37, –0.34
˚
Dqmax, Dqmin (e A
)
CCDC deposition no.
977339
Results and Discussion
Single Crystal X-ray Diffraction
Tripeptide 4 was prepared in accordance with our previ-
ously optimised procedures [30, 31]: first, hydrogenolytic
N-deprotection of dipeptide 5 [33] in the presence of
Pearlman’s catalyst [Pd(OH)2/C] under an atmosphere of
H2 gave dimer amine 6 in 92 % isolated yield. Coupling of
6 with monomer acid 8 ([99:1 dr) [34] was achieved with
HOBt/EDCÁHCl to give trimer 7 as a single diastereoiso-
mer ([99:1 dr) in 58 % yield after purification of the crude
reaction mixture via recrystallisation (CHCl3/heptane).
Subsequent treatment of trimer 7 with TFA gave Cbz-
[(1R,2S)-ACPC]3-OH 4 in 70 % yield and [99:1 dr
(Scheme 1). Recrystallisation of 4 from CHCl3/heptane
gave colourless plates which were subjected to X-ray dif-
fraction analysis.
Single crystal diffraction data for tripeptide 4 were col-
lected using a Nonius j-CCD diffractometer (Mo-Ka
radiation, k = 0.71073 A) at 150(2) K with an Oxford
˚
Cryosystems Cryostream N2 open-flow cooling device
[35]. Raw frame data were processed using the DENZO-
SMN package [36], including unit cell parameter refine-
ment and inter-frame scaling (which were carried out using
SCALEPACK within DENZO-SMN). The structure was
solved using SIR92 [37] and refinement was carried out
using full-matrix least-squares within the CRYSTALS
suite [38], on F2. All non-hydrogen atoms were refined
with anisotropic displacement parameters. The positions
and isotropic displacement parameters of hydrogen atoms
were refined using restraints prior to inclusion into the
model with riding constraints [39]. In the absence of a
significant anomalous signal, the Friedel pairs were merged
for the final refinement.
The molecular structure of 4 is illustrated below
(Fig. 2). Adjacent molecules are linked by a series of
intermolecular N–HÁÁÁO=C and O–HÁÁÁO=C hydrogen
bonds to form a double tape-like arrangement in the crystal
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J Chem Crystallogr (2014) 44:205–209
Fig. 2 Molecular structure of 4,
showing the displacement
ellipsoids drawn at the 50 %
probability level
pentamers which were suitable for X-ray crystallographic
1
analyses, a combination of IR, H NMR and CD spectro-
scopic analyses confirmed that these oligomers display
traits indicative of intermolecular hydrogen bonding [32]
and are therefore consistent with a similar conformation in
solution.
Conclusion
In conclusion, the crystal structure of the b-peptide Cbz-
[(1R,2S)-ACPC]3-OH, which is derived from (1R,2S)-
cispentacin, was studied by X-ray diffraction. Adjacent
molecules are linked by a series of N–HÁÁÁO=C and
O–HÁÁÁO=C hydrogen bonds to form a double tape-like
arrangement in the solid state.
Fig. 3 H-bonding within the crystal structure of 4, viewed along the
a axis; selected H atoms are omitted for clarity. Hydrogen bonding
interactions are shown as grey dotted lines, forming R2,2(14)
intermolecular rings [40] that connect molecules together to give
hydrogen bonded peptide chains [N–HÁÁÁO=2.998(4), 3.240(4),
Supporting Information
Full crystallographic data for 4 have been deposited with
the Cambridge Crystallographic Data Centre as supple-
mentary publication number CCDC 977339. Copies of
these data can be obtained free of charge from The Cam-
bridge Crystallographic Data Centre via www.ccdc.cam.ac.
uk/data_request/cif.
˚
˚
2.869(4) A; O–HÁÁÁO=2.579(4) A]
structure consisting of R2,2(10) and R2,2(14) intermolec-
ular rings (Figs. 3 and 4) [40]. Whilst it was not possible to
produce crystals of the corresponding tetramers or
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J Chem Crystallogr (2014) 44:205–209
209
Fig. 4 H-bonding within the
crystal structure of 4, viewed
perpendicular to the a axis;
selected H atoms are omitted for
clarity. Hydrogen bonding
interactions are shown as grey
dotted lines, forming R2,2(10)
intermolecular rings [40] that
connect together to give
hydrogen bonded peptide chains
[N–HÁÁÁO=2.998(4), 3.240(4),
˚
2.869(4) A; O–HÁÁÁO=2.579(4)
˚
A]
22. Seebach D, Abele S, Schreiber JV, Martinoni B, Nussbaum AK,
Schild H, Schulz H, Hennecke H, Woessner R, Bitsch F (1998)
Chimia 52:734
¨
23. Seebach D, Hook DF, Glatti A (2006) Biopolymers (Peptide
Science) 84:23
24. Aguilar M-I, Purcell AW, Devi R, Lew R, Rossjohn J, Smith I,
Perlmutter P (2007) Org Biomol Chem 5:2884
25. Werder M, Hauser H, Abele S, Seebach D (1999) Helv Chim
Acta 82:1774
References
1. Hintermann T, Seebach D (1997) Synlett 437
2. Seebach D, Abele S, Gademann K, Guichard G, Hintermann T,
Jaun B, Matthews JL, Schreiber JV (1998) Helv Chim Acta
81:932
3. Gung BW, Zou D (1999) J Org Chem 64:2176
4. Raguse L, Lai JR, Gellman SH (2002) Helv Chim Acta 85:4154
¨
5. Glattli A, Seebach D, van Gunsteren WF (2004) Helv Chim Acta
87:24872
26. Hamuro Y, Schneider JP, DeGrado WF (1999) J Am Chem Soc
121:12200
6. Luppi G, Galeazzi R, Garavelli M, Formaggio F, Tomasini C
(2004) Org Biomol Chem 2:2187
7. Izquierdo S, Kogan MJ, Parella T, Moglioni AG, Branchadell V,
Giralt E, Ortun˜o RM (2004) J Org Chem 69:5093
8. Appella DH, Christianson LA, Karle IL, Powell DR, Gellman SH
(1996) J Am Chem Soc 118:13071
9. Barchi JJ Jr, Huang X, Appella DH, Christianson LA, Durell SR,
Gellman SH (2000) J Am Chem Soc 122:2711
10. Applequist J, Bode KA, Appella DH, Christianson LA, Gellman
SH (1998) J Am Chem Soc 120:4891
11. Wang X, Espinosa JF, Gellman SH (2000) J Am Chem Soc
122:4821
12. Lee H-S, Syud FA, Wang X, Gellman SH (2001) J Am Chem Soc
123:7721
13. Winkler JD, Piatnitski EL, Mehlmann J, Kasparec J, Axelsen PH
(2001) Angew Chem Int Ed 40:743
14. Woll MG, Fisk JD, LePlae PR, Gellman SH (2002) J Am Chem
Soc 124:12447
15. Raguse L, Lai JR, Gellman SH (2003) J Am Chem Soc 125:5592
16. Park J-S, Lee H-S, Lai JR, Kim BM, Gellman SH (2003) J Am
Chem Soc 125:8539
27. Liu D, DeGrado WF (2001) J Am Chem Soc 123:7553
28. Appella DH, Christianson LA, Klein DA, Powell DR, Huang X,
Barchi JJ Jr, Gellman SH (1997) Nature 387:381
29. For a review, see: Fu¨lop F (2001) Chem Rev 101:2181
30. Abraham E, Bailey CW, Claridge TDW, Davies SG, Ling KB,
Odell B, Rees TL, Roberts PM, Russell AJ, Smith AD, Smith LJ,
Storr HR, Sweet MJ, Thompson AL, Thomson JE, Tranter GE,
Watkin DJ (2010) Tetrahedron: Asymmetry 21:1797
31. Abraham E, Claridge TDW, Davies SG, Odell B, Roberts PM,
Russell AJ, Smith AD, Smith LJ, Storr HR, Sweet MJ, Thomson
JE, Thompson AL, Tranter GE, Watkin DJ (2011) Tetrahedron:
Asymmetry 22:69
´
´
32. Martinek TA, Toth GK, Vaas E, Hollosi M, Fu¨lop F (2002)
¨
Angew Chem Int Ed 41:1718
33. Abraham E, Davies SG, Roberts PM, Thompson AL, Thomson
JE (2011) J Chem Crystallogr 41:1722
34. Davies SG, Russell AJ, Sheppard RL, Smith AD, Thomson JE
(2007) Org Biomol Chem 5:3190
35. Cosier J, Glazer AM (1986) J Appl Crystallogr 19:105
36. Otwinowski Z, Minor W (1997) Methods Enzymol. Academic
Press, New York, pp 307–326
37. Altomare A, Cascarano G, Giacovazzo C, Guagliardi A, Burla
MC, Polidori G, Camalli M (1994) J Appl Crystallogr 27:435
38. Betteridge PW, Carruthers JR, Cooper GI, Prout CK, Watkin DJ
(2003) J Appl Crystallogr 36:1487
17. Peelen TJ, Chi Y, English EP, Gellman SH (2004) Org Lett
6:4411
18. Simpson GL, Gordon AH, Lindsay DM, Promsawan N, Crump
MP, Mulholland K, Hayter BR, Gallagher T (2006) J Am Chem
Soc 128:10638
39. Cooper RI, Thompson AL, Watkin DJ (2010) J Appl Cryst
43:1100
40. Bernstein J, Davis RE, Shimoni L, Chang N-L (1995) Angew
Chem Int Ed 34:1555
´
´
´
¨
19. Martinek TA, Mandity IM, Fu¨lop L, Toth GK, Vaas E, Hollosi
´
¨
M, Forro E, Fu¨lop F (2006) J Am Chem Soc 128:13539
20. Seebach D, Overhand M, Kuhnle FNM, Martinoni B, Oberer L,
Hommel U, Widmer H (1996) Helv Chim Acta 79:913
21. Hintermann T, Seebach D (1997) Chimia 50:244
123