Progress towards the synthesis of piperazimycin A: synthesis of the non-proteogenic amino acids and elaboration into dipeptides

Article abstract of DOI:10.1016/j.tetlet.2010.02.168

This Letter describes the synthesis of the five non-proteogenic amino acids required for the total synthesis of piperazimycin A, and synthetic elaboration into multiple dipeptides. Importantly, this Letter details the first example of an elusive piperazic acid-piperazic acid coupling to form this key C5-C14 dipeptide.

Full text of DOI:10.1016/j.tetlet.2010.02.168

Tetrahedron Letters 51 (2010) 2493–2496
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Progress towards the synthesis of piperazimycin A: synthesis
of the non-proteogenic amino acids and elaboration into dipeptides
*
J. Phillip Kennedy, Craig W. Lindsley
Department of Chemistry and Pharmacology, Vanderbilt Program in Drug Discovery, Vanderbilt Institute of Chemical Biology, Vanderbilt University,
Vanderbilt Medical Center, Nashville, TN 37232, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
This Letter describes the synthesis of the five non-proteogenic amino acids required for the total synthe-
sis of piperazimycin A, and synthetic elaboration into multiple dipeptides. Importantly, this Letter details
the first example of an elusive piperazic acid–piperazic acid coupling to form this key C5–C14 dipeptide.
Ó 2010 Elsevier Ltd. All rights reserved.
Received 22 January 2010
Revised 24 February 2010
Accepted 26 February 2010
Available online 3 March 2010
Fenical and co-workers recently reported on the isolation of pip-
erazimycin A 1 from the fermentation broth of a Streptomyces sp.,
cultivated from marine sediments near the island of Guam.1 A cyclic
hexadepsipeptide, 1 is composed of rare amino acids such as
hydroxyacetic acid (HAA),
methyl-4,6-nonadecadienoic acid (AMNA), two
acids ((S,S)- OHPip and (R,R)- OHPip and one
acid (R,S)-
ClPip (Fig. 1).1 Piperazimycin A (1) proved to be a potent
a
-methylserine, a novel (S)-2-amino-8-
-hydroxypiperazic
-chloropiperazic
c
c
c
c
c
cancer cell cytotoxin which exhibited in vitro cytotoxicity towards
multiple tumour cell lines with a mean GI50 of 100 nM.1 Based on
its novel molecular architecture, the diversity of non-proteogenic
amino acid building blocks and its potent cytotoxicity, we embarked
on a total synthesis campaign targeting piperazimycin A (1) in suffi-
cient quantities to elucidate and pursue chemical biology studies.2
In light of a recent total synthesis of piperazimycin A by Ma and
co-workers (they coupled acyclic peptides and then cyclized to form
the piperazic acids),3 we describe here our progress towards piper-
azimycin A via fundamentally different synthetic approaches for
the synthesis of both individual amino acids and dipeptides as well
as the first example of a successful piperazic acid-piperazic acid
coupling.
Figure 1. Structure of Piperazimycin A (1) and retrosynthetic plan.
In order to complete a total synthesis of 1, we first had to synthe-
size the requisite non-proteogenic amino acids 2–6 (Fig. 2). In a re-
cent Letter, we described the synthesis of two
acids, (R,R)- OHPip 9 and (S,S)- OHPip 10 and one
ic acid (R,S)- ClPip 11 starting from either (R)- or (S)-4-chloro-3-
c-hydroxypiperazic
c
c
c-chloropiperaz-
c
hydroxybutanoic acid ethyl ester, 7 and 8, respectively, in 8–9 steps
via a key asymmetric Strecker reaction (Scheme 1).2 For our current
effort, we followed this route, but prepared Teoc derivatives 12–14
in place of the aforementioned Alloc congeners 9–11. Overall yields
for the eight step synthesis of 12 and 13 averaged 65%, and 14 was
obtained in nine steps and 22% overall yield.
* Corresponding author. Tel.: +1 615 322 8700; fax: +1 615 343 6532.
E-mail address: craig.lindsley@vanderbilt.edu (C.W. Lindsley).
Figure 2. Non-proteogenic amino acids target molecules 2–6.
0040-4039/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2010.02.168

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J. Phillip Kennedy, C. W. Lindsley / Tetrahedron Letters 51 (2010) 2493–2496
yield. Ozonolysis delivers aldehyde 25 in 53% yield, and delivers
one component for the envisioned Julia–Kocienski olefination8–10
to provide the (E,E)-stereochemistry in 5. The second component
was derived from the commercially available (E)-methyl-4-meth-
ylpent-2-enoate 26. Reduction with DIBALH provides, after distilla-
tion, allylic alcohol 27 in 75% yield. Deprotonation with n-BuLi,
conversion to the tosylate and displacement of the allylic tosylate
with the thiotetrazole and oxidation affords 28 in 53% yield for the
four steps. The Julia–Kocienski olefination proceeds by deprotona-
tion of 28 with KHMDS in DMF/HMPA to provide an 80:20 mixture
of E/Z isomers.8–10 Exposure to iodine and UV light isomerizes the
diene to >95:5 E/Z. Deprotection of the Boc group with HCl delivers
the bench stable AMNA congener, 29 in 70% yield for the three
steps. 29 was also protected with the Troc group and the ester
hydrolyzed to afford congener 30.
Finally, we prepared the protected forms of
a-methyl serine
amino acid 6 for subsequent coupling (Scheme 4). Commercial
(S)-2-amino-3-hydroxy-2-methylpropanoic acid 6 was Boc pro-
tected, followed by protection of the primary hydroxyl as a
TBDPS ether to deliver 31 in 98% for the two steps. Compound
31 was then further elaborated with the HAA moiety to pro-
vide 32 to complete the northeastern fragment of piperazimy-
cin A 1.
Scheme 1. Synthesis of N-protected, c-substituted piperazic acids 9–14.
With all the non-proteogenic amino acid components prepared,
effort focused on construction of key dipeptides en route to a total
synthesis of 1. As described by Ma,3 the peptide couplings were not
trivial and each had to be optimized independently surveying doz-
ens of coupling reagents, additives, solvents and alternative pro-
tecting groups on the various amino acid congeners of 2–6. In
the recently reported total synthesis of 1 by Ma,3 they state that
they were unable to affect the never before described piperazic
acid-piperazic acid coupling between suitable congeners of 13
and 14. Thus in their work, they followed the Danishefsky ap-
proach,4–6 coupling acyclic amino acids and then cyclizing to form
the piperazic acids as shown in Scheme 2. In our hands, we also
were unable to couple analogues of 13 and 14; however, protecting
groups proved to be the key for this difficult transformation. Thus,
From our experience thus far with piperazic acids, we also re-
quired a bis-Boc congener 22 to explore amide coupling condi-
tions en route to
a total synthesis of 1. To this end, we
followed a variation of Danishevsky’s published route (Scheme
2).4–6 Starting with the commercial (S)-lactone 15, opening with
methoxide, followed by conversion of the primary hydroxyl to
the bromide affords 16 in 45% yield for the two steps. TBS protec-
tion of the secondary hydroxyl, followed by enolate formation
and trapping with di-tert-butyl azodicarboxylate (DBAD) provides
17, in 56% yield for the two steps. Deprotonation with NaH and
cyclization delivers a 1:1 diastereomeric mixture of piperazic es-
ters 18. Careful column chromatography delivers (R,S)-
19 in 40% yield. Removal of the TBS group, application of the
Hale protocol7 to install the
-chloro functionality and hydrolysis
cJTBSPip
the bis-Boc c-ClPip 22 was successfully coupled to 13 in 62% yield
c
employing freshly made tetramethyl chloroformamidinium hexa-
fluorophosphate (TCFH), to form the acid chloride in situ, and pro-
vide 33, and the first example of a piperazic acid-piperazic acid
coupling (Scheme 5). The Boc groups were then removed with
TFA and subsequent Teoc protection provided 34, albeit in low
yield (12% for the two steps).11 Thus, the southern C5–C14 piperaz-
ic acid-piperazic acid fragment was prepared. However, we have
provided the target 22 in 45% yield for the three steps. Overall,
the eight-step sequence proceeded in 4.6% yield on multi-gram
scales.
With all the requisite c-substituted piperazic acids 12–14 and
22 in hand, attention now focused on preparing the unnatural
AMNA, 5 (Scheme 3). Beginning with a commercial (S)-allyl glycine
derivative 23, Boc protection and esterification affords 24 in 96%
Scheme 2. Reagents and conditions: (a) (i) NaOMe, MeOH, (ii) LiBr, THF, HOAc, 45% for the two steps; (b) (i) TBSOTf, Imid, DMF, (ii) NaHMDS, THF, DBAD, 56% for the two
steps; (c) NaH, DMF; (d) column chromatography, 40% over two (c and d) steps; (e) (i) 1 M TBAF, THF, 0 °C, (ii) NCS, PPh3, DCM, (iii) 2 M LiOH, THF, 0 °C to rt, 45% for the three
steps.

J. Phillip Kennedy, C. W. Lindsley / Tetrahedron Letters 51 (2010) 2493–2496
2495
Scheme 5. Reagents and conditions: (a) 13, TCFH, DCM, collidine, 0 °C to rt, 62%; (b)
(i) TFA, DCM, 0 °C to rt, (ii) TeocCl, DMF, DIEA, 12% for two steps.
Scheme 3. Reagents and conditions: (a) (i) Boc2O, TEA:DCM, (ii) MeI, TEA:DCM, 96%
for two steps; (b) (i) O3, DCM, À78 °C, (ii) DMS, 53%; (c) 2.2 equiv DIBALH, Et2O,
À78 °C, distillation, 75%; (d) (i) n-BuLi, 0 °C, (ii) TosCl, (iii) sodium 1-phenyl-1H-
tetrazole-5-thiolate, 72% for three steps; (e) molybdenum, H2O2, EtOH, 98%; (f) (i)
KHMDS, HMPA, DMF, (ii) 25, (iii) I2, UV light, Et2O, HCl (g), 70% for three steps; (g) (i)
TrocCl, DCM, TEA, (ii) 2 M LiOH, THF, 0 °C to rt, 90% for the two steps.
not been able to identify any conditions or protecting groups that
allow 34 to be further elaborated.
To construct the eastern half of 1, the Boc group of 32 was che-
moselectively removed with HCl(g) in EtOAc to deliver 35, which
was then coupled to 36, a hydrolyzed congener of 13, under the
standard HATU coupling conditions to deliver 37 in 26% yield for
the two steps (Scheme 6).
In parallel, the Troc-protected AMNA 30 was coupled to 14 un-
der TCFH conditions (all others failed entirely) to deliver this
dipeptide 38 in 49% yield. Hydrolysis generated 39 in a quantita-
tive yield (Scheme 7).
The northwestern portion of 1 was also prepared (Scheme 8).
OHPip 12 was coupled to a PMB protected HAA congener 40 to
Scheme 6. Reagents and conditions: (a) HCl(g), EtOAc, 0 °C to rt, 100%; (b) (i) HATU,
HOAt, DCM, collidine, 26%.
c
provide 41 in 87% yield. Hydrolysis, subsequent HATU-mediated
coupling with AMNA congener 29 and a second hydrolysis led to
dipeptide 42 in 60% yield for the three steps. However, our most
optimal coupling conditions thus far has proven ineffective to fur-
ther elaborate any of the dipeptide fragments 34, 37, 39 or 42. In
order to complete the total synthesis of 1, we will need to evaluate
a more diverse array of peptide coupling strategies in combination
with a diverse range of nitrogen-protecting groups on key peptide
and dipeptide fragments.
Importantly, we report on the first successful piperazic acid-piper-
azic acid coupling, mediated by TCFH, to synthesize the southern
(R,S)-cClPip-(S,S)-cOHPip dipeptide 34. We report our progress to-
wards 1 due to the recent total synthesis reported by Ma and co-
workers; moreover, our routes are fundamentally different for
the synthesis of the individual non-proteogenic amino acids 2–6
found in piperazimycin A, and our approach to the dipeptide syn-
thesis. Further refinements are underway towards a total synthesis
of 1 and the related piperazimycin B, and will be reported in due
course.
In summary, we have synthesized all five of the non-proteo-
genic amino acids found in piperazimycin A 1, and synthesized
four advanced dipeptides (two with the HAA motif attached).
Scheme 4. Reagents and conditions: (a) (i) Boc2O, TEA/DCM, (ii) TBDPSCl, imidazole, DMF, 98% for two steps; (b) NaH, Bromoacetic acid methyl ester 80%.

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J. Phillip Kennedy, C. W. Lindsley / Tetrahedron Letters 51 (2010) 2493–2496
Scheme 7. Reagents and conditions: (a) TCFH, DCM, collidine, 0 °C to rt, 49%; (b) 2 M LiOH, THF, 0 °C to rt, quantitative.
Scheme 8. Reagents and conditions: (a) TCFH, DCM, collidine, 0 °C to rt, 87%; (b) (i) 2 M LiOH, THF, 0 °C to rt, 99%, (ii) HATU, HOAt, collidine, DCM, 62%, (iii) 2 M LiOH, THF,
0 °C to rt, 99%.
8. Blakemore, P. R.; Cole, W. J.; Kocienski, P. J.; Morley, A. Synlett 1998, 26–28.
9. Blakemore, P. R.; Ho, D. K. H.; Nap, W. M. Org. Biomol. Chem. 2005, 3, 1365–
Acknowledgements
1368.
The authors thank the Department of Pharmacology at Vander-
bilt and the Vanderbilt Institute of Chemical Biology (VICB) for sup-
port of this research. J.P.K. thanks the VICB for a generous
predoctoral fellowship.
10. Pospisil, J.; Marko, I. E. Org. Lett. 2006, 8, 5983–5986.
11. Experimental for the synthesis of 33: A flame-dried 50 ml flask outfitted with a
stirbar was charged with acid 22 (160 mg, 0.439 mmol), and amine 13
(184 mg, 0.439 mmol) was vacuum purged 3x with argon. DCM (10 ml)
followed by collidine (175 ll, 1.32 mmol) was added and the reaction was
stirred until homogeneous. Freshly made TCFH (246 mg, 0.878 mmol) was
added all at once and the reaction was stirred overnight. Once determined
complete by LC/MS and TLC the reaction was quenched with H2O and NaHCO3
and the reaction mixture was extracted with DCM 3x. The organic layer was
dried with MgSO4, filtered and concentrated to afford the crude material which
was purified by silica gel chromatography (EtOAc/Hex 1:3) to afford pure 33 in
62% yield (207 mg, 0.272 mmol). 1H NMR (400 MHz, CDCl3) d 5.15 (m, 1H), 5.10
(m, 1H), 4.27 (m, 1H), 4.10 (m, 2H), 4.00 (m, 1H), 3.67 (s, 3H), 2.92 (m, 1H), 2.50
(m, 1H), 2.22 (m, 1H), 1.78 (m, 2H), 1.60 (m, 2H), 1.59 (s, 3H), 1.44 (s, 3H), 1.42
(s, 18H), 1.30 (m, 2H), 1.06 (m, 1H), 0.90 (s, 9H), 0.05 (s, 9H). 13C NMR
(100 MHz, CDCl3) d 170.4, 155.8, 153.2, 81.8, 64.9, 63.5, 51.9, 49.6, 48.8, 34.5,
31.7, 30.3, 29.7, 28.3, 26.9, 25.7, 25.3, 22.6, 20.7, 18.3, 14.1, À1.6, À5.1. HRMS
(Q-ToF): m/z calcd for C33H61N4O10NaSi2Cl [M+Na] 787.3528, found 787.3512.
References and notes
1. Miller, E. D.; Kauffma, C. A.; Jensen, P. R.; Fenical, W. J. Org. Chem. 2007, 72, 323–
330.
2. Kennedy, J. P.; Brogan, J. T.; Lindsley, C. W. Tetrahedron Lett. 2008, 49, 4116–4118.
3. Li, W.; Gan, J.; Ma, D. Angew. Chem., Int. Ed. 2009, 48, 8891–8895.
4. Kamenecka, T. M.; Danishefsky, S. J. Angew. Chem., Int. Ed. 1998, 37, 2995–2998.
5. Depew, K. M.; Kamenecka, T. M.; Danishefsky, S. J. Tetrahedron Lett. 2000, 41,
289–292.
6. Kamenecka, T. M.; Danishefsky, S. J. Chem. A Eur. J. 2001, 7, 41–63.
7. Hale, K. J.; Jogiya, N.; Manaviazar, S. Tetrahedron Lett. 1998, 39, 7163–7166.