α-amino acid Troeger base derivatives, possible conformationally restricted scaffolds?

Article abstract of DOI:10.1039/b614371g

The first synthesis of innovative α-amino acid conjugates of Troeger base is reported; their potential application as conformationally restricted scaffolds is proposed and has been investigated using high level ab initio calculations. The Royal Society of Chemistry.

Full text of DOI:10.1039/b614371g

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a-Amino acid Tro¨ger base derivatives, possible conformationally
restricted scaffolds?{{
Sean P. Bew,* Laurent Legentil, Vincent Scholier and Sunil V. Sharma
Received (in Cambridge, UK) 4th October 2006, Accepted 7th December 2006
First published as an Advance Article on the web 15th December 2006
DOI: 10.1039/b614371g
The first synthesis of innovative a-amino acid conjugates of
Tro¨ger base is reported; their potential application as con-
formationally restricted scaffolds is proposed and has been
investigated using high level ab initio calculations.
We report studies on 2,8-bis-a-amino acid Tro¨ger base adducts (1,
Fig. 1) and propose them as scaffolds for use as peptide chain
directors i.e. 2. Tro¨ger base1 is a C2-symmetric heterocycle with a
relatively rigid backbone, hydrophobic cavity and concave
conformation. Due to its sharply folded geometry the aryl rings
reside in a near perpendicular arrangement (generally 90–100u).2
Gaining insights into the biological mode of action of natural/
Fig. 2 Chem 3D representation of bis-2,8-(N,C-protected a-amino acid)
Tro¨ger base adduct 3.
non-natural proteins, polypeptides and enzymes is critical if a
couplings.8 However, the synthesis of milligram quantities of
comprehensive understanding of protein action is to be acquired.
racemic bis-2,8-diiodo 4 has been reported by Wa¨rnmark et al.7
In this respect many studies have been undertaken on the
Translating this protocol directly to the production of multigram
application/development of innovative mimics of b-turns and
quantities of 4 was problematic with low yields (y10%) resulting.
hairpins.3 The synthesis of an a-amino acid derived Tro¨ger base
After careful optimisation of the experimental and purification
scaffold4 and its appendage with additional a-amino acid
procedures we were able to accrue multigram quantities of racemic
derivatives affords a new opportunity to investigate the loop and
4 in y46% yield. Employing a single enantiomer of 4 would
hinge regions of proteins. a-Amino acid Tro¨ger base derivatives
significantly simplify the analysis of the resulting diastereomeric
similar to 3 (Fig. 2) appear not only to be able to act as scaffolds,
a-amino acid Tro¨ger base conjugates. That said, all our attempts at
but also to have the capacity to direct appended peptides within a
resolving 4 using literature protocols failed.8 Undeterred, we
90–100u range. Small peptide chains have been identified that
transformed racemic 4 into bis-2,8-dialkyne 5 via a Sonogashira
contain 90–100u bends. For example, the polypeptide
TNYLFSPNGPIARAW that binds to EphB4 (IC50 15 nM)
coupling with TMSA. Desilylation of 5 using TBAF afforded 6 in
a poor 23% yield. Switching to sodium hydroxide in a methanol–
embodies a 90u turn induced by the GP dipeptide. This turn within
the pentadecapeptide is critical for high affinity binding of the
THF mix negated this problem; an excellent 91% yield of
bis-2,8-ethynyl
6 resulted. Coupling 6 with 4-iodo-N-Boc-
polypeptide into the hydrophobic upper convex portion of the
active site within EphB4.5
(S)-phenylalanine methyl ester 7 was attempted. Utilising standard
Sonogashira coupling conditions either no reaction took place or
poor yields of 9 resulted (y15%). Gratifyingly, when DMF was
employed, and freshly synthesised tetrakis(triphenylphosphine)pal-
ladium(0) and 2.2 equiv. of 7 were utilised the desired Tro¨ger base
adduct 9 was returned in an unoptimised 60% yield (Scheme 1).
The transition-metal mediated synthesis of adducts based on 3
requires a practical, efficient and convenient synthesis of building
block 4 (Scheme 1).6 The bis-2,8-dibromo analog of 4 was not
considered due to its recalcitrant nature towards Sonogashira
Fig. 1 a-Amino acid Tro¨ger base scaffolds as peptide chain directors.
School of Chemical Sciences & Pharmacy, University of East Anglia,
Norwich, Norfolk, UK NR4 7TJ. E-mail: s.bew@uea.ac.uk;
Fax: 44 (0)1603 592003; Tel: 44(0)1603 593142
{ Electronic supplementary information (ESI) available: Experimental
details. See DOI: 10.1039/b614371g
{ The HTML version of this article has been enhanced with colour
images.
Scheme 1 Synthesis of 2,8-difunctionalised Tro¨ger base adducts.
Chem. Commun., 2007, 389–391 | 389
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Curiously, attempting to couple
4 and N-Boc-4-ethynyl-
(S)-phenylalanine methyl ester (8) using the previously successful
Sonogashira reaction conditions for 6 and 7 i.e. DMF, Et3N, CuI,
Pd(PPh3)4, failed to return any 9.
We considered the possibility that the transition-metal mediated
coupling reaction between (S)-7 and racemic 4 may result in a
chiral resolution of racemic 4 affording diastereomerically enriched
9. Subjecting 9 to chiral HPLC analysis (Chiralpack AD, 24 6
0.46 cm) clearly showed the (S,S,S)- and (S,R,S)-9 adducts in an
equal ratio.9 Our attempts at separating, using flash chromato-
graphy, (S,S,S)- and (S,R,S)-9 failed. Similar separation problems
with different Tro¨ger base adducts have been reported by Maitra
et al.10
The synthesis of an alicyclic, bis-2,8-(N,C-protected)-a-amino
acid Tro¨ger base was attempted. Incorporating 4, N-Boc-
(S)-propargylglycine ethyl ester (2.5 equivalents) and the reaction
conditions/catalysts employed to couple 6 and 7 (Scheme 1), we
were surprised to find that from the myriad of by- and
decomposition products the desired adduct 10 (Fig. 3) was
afforded in a disappointing 10% yield; furthermore we also
isolated, albeit in mediocre 28% yield, the corresponding 2-(N-Boc-
(S)-propargylglycine ethyl ester)-8-iodo Tro¨ger base.
Scheme 2 Synthesis of Tro¨ger base 13.
4 and N-Boc-(S)-propargylglycine ethyl ester
procedure,
(1 equivalent each) we isolated the desired mono a-amino acid
coupled 8-iodo-Tro¨ger base adduct in an unoptimised 56% yield.
Subjecting this to a second Sonogashira coupling with TMSA
[PdCl2(PPh3)2, Et3N, CuI, THF] and subsequent desilylation
afforded 15 which was readily coupled to 14 affording the fully
differentially N,C-protected a-amino acid derived Tro¨ger base 16
(Scheme 3). With this important adduct in hand its chemoselective
TMSE C-deprotection was undertaken using TBAF; the resulting
carboxylic acid was coupled to (S)-valine methyl ester affording
Hydrogenation (5% Pd on C, H2, MeOH, 1 atmosphere) of the
rigid bis-2,8-ethynyl linkers within 9 and 10 afforded, in
quantitative yields, the corresponding alkane linked adducts 12
and 11 respectively. The reported sensitivity of Tro¨ger base to
acidic conditions2a compelled us to check the feasibility of
performing an acid mediated N-Boc deprotection. Gratifyingly,
reacting 11 or 12 with TFA cleanly removed all the N-Boc groups
(79% and 82% yields respectively) affording the corresponding
TFA salts. Liberation of the free amine (Et3N) from the TFA salt
of N-deprotected 12 followed by 1H-NMR analysis confirmed the
Tro¨ger base heterocycle to be intact. Testing the concept that
additional a-amino acids can be readily appended, tetrapeptide 13
was synthesised in an excellent 89% yield (Scheme 2).
As part of our wider strategy towards utilising Tro¨ger base as a
scaffold we sought to append two differentially N,C-protected-
a-amino acids onto one Tro¨ger base. The possibility of
chemoselectively cleaving, when desired, one of the four N- or
C-protecting groups off one of the a-amino acids would
significantly enhance the potential of the Tro¨ger base scaffolds.
Disappointingly, utilising 6, one equivalent of 7 and the catalyst/
reaction conditions outlined in Scheme 1 failed to afford any
significant amounts of the desired mono-a-amino acid appended
adduct. A complex mixture of products comprising: starting
material 6, homocoupled bis-alkynyls, bis-2,8-alkynyl Tro¨ger base
adduct i.e. 9 as well as unidentifiable by-products resulted.
Buchwald et al.11 and Wa¨rnmark et al.7 have reported on an
unusually reactive Sonogashira protocol for the efficient coupling
of electron-rich aryl halides and alkynes that employs catalytic
amounts of tri-tert-butylphosphine (10%). Utilising Wa¨rnmark’s
Fig. 3 Bis-2,8-[N-Boc-(S)-propargylglycine ethyl ester] Tro¨ger base.
390 | Chem. Commun., 2007, 389–391
Scheme 3 Synthesis of Tro¨ger base derived tetrapeptides 18 and 19.
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a-amino acids, holding them to a near perpendicular angle
(calculated aryl plane angle of 100.83u). Furthermore, and of
importance for application as a scaffold, the DFT calculation
suggests that the N- and C-terminated a-amino acid ‘arms’ are
projected along the aryl planes of the Tro¨ger base.
In summary, we have developed a novel strategy for the
synthesis of structurally unique bis-(N,C-protected-a-amino acid)
derived Tro¨ger base adducts. Using chemoselective N- or
C-a-amino acid deprotection strategies we have demonstrated
the feasibility of synthesising non-symmetric Tro¨ger base tetra-
peptides. Our hypothesis that Tro¨ger base adducts can be
employed as new conformationally restricted scaffolds has been
reinforced by high level ab initio calculations.
Fig. 4 Calculated (using B3LYP/6-31G) conformation of 11 and tert-
butyl Tro¨ger base edge-to-face interactions reported by Wilcox et al.
SPB would like to thank Pfizer, The University of East Anglia
(VS), the Dovetrust (SVS), and the EPSRC for funding (LL) and
Professor Floris Rutjers (University of Nijmegen) for a gift of
(S)-propargylglycine.
Notes and references
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3 N. Sewald and H.-D. Jakubke, Peptides: Chemistry and Biology, Wiley-
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Fig. 5 Calculated conformation using B3LYP/6-31G basis set.
5 K. D. Stigers, M. J. Soth and J. S. Nowick, Curr. Opin. Chem. Biol.,
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tripeptide 17 in a 60% yield. Chemoselective cleavage of the N-Boc
group off 17 (TFA, 83%) and subsequent appendage of (N)-Boc-
(S)-histidine afforded Tro¨ger base tetrapeptide 18, which under-
went hydrogenation affording 19.
With the potential application of the a-amino acid Tro¨ger base
conjugates as scaffolds in mind we sought corroboration of their
conformation. Despite an intensive effort we have been unable to
grow crystals of 11–13 or 19 suitable for X-ray analysis,
furthermore NOE experiments were unproductive.
Employing ab initio DFT calculations Stephens et al.12 predicted
the conformations of a series of Tro¨ger base adducts and
compared their results with X-ray crystal structures deposited in
the CSD. The agreement of theory and experiment was excellent.
Using Gaussian 9813 (B3LYP functional level and 6-31G basis set)
an energy minimisation performed on the relatively simple adduct
11 revealed an unusual ‘bite back’ of one of the N-Boc groups such
that the tert-butyl moiety undergoes edge-to-face aryl–alkyl
interactions (Fig. 4). Interestingly, and in agreement with our
calculations, Wilcox et al. observed similar molecular recognition
forces in ‘Tilted-T’ Tro¨ger base derivatives. Indeed Wilcox et al.
reported that alkyl tert-butyl ester 20 had a ‘strong preference,
greater than any aryl ester, for the formation of edge-to-face
interactions’.14
12 A. Aamouche, F. J. Devlin and P. J. Stephens, J. Am. Chem. Soc., 2000,
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To test our concept that a-amino acid Tro¨ger base conjugates
may be capable of acting as conformationally restrictive scaffolds
we subjected N-Cbz derived 19 to ab initio DFT calculations
(B3LYP and 6-31G). Gratifyingly, the calculations indicate (Fig. 5)
that the Tro¨ger base scaffold does indeed constrain appended
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