Skeletal diversity by sequential one-pot and stepwise routes using morpholine ester scaffolds

Article abstract of DOI:10.1016/j.tetlet.2010.09.103

A skeletal diversity approach starting from morpholine acetals has been achieved by tuning a three-step process from stepwise to sequential one-pot to provide diverse scaffolds containing either a 2-oxopiperazine or a diketopiperazine skeleton.

Full text of DOI:10.1016/j.tetlet.2010.09.103

Tetrahedron Letters 51 (2010) 6282–6285
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Skeletal diversity by sequential one-pot and stepwise routes using
morpholine ester scaffolds
Leonardo Ciofi a, Manfredi Morvillo a, Filippo Sladojevich b, Antonio Guarna a, Andrea Trabocchi a,
⇑
a Department of Chemistry ‘Ugo Schiff’, University of Florence, Polo Scientifico e Tecnologico, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Florence, Italy
b Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
a r t i c l e i n f o
a b s t r a c t
Article history:
A skeletal diversity approach starting from morpholine acetals has been achieved by tuning a three-step
process from stepwise to sequential one-pot to provide diverse scaffolds containing either a 2-oxopiper-
azine or a diketopiperazine skeleton.
Received 18 August 2010
Accepted 20 September 2010
Available online 29 September 2010
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
Chemical diversity
Amino acids
Peptidomimetics
Combinatorial Chemistry
Heterocycles
Diversity-Oriented Synthesis (DOS)1 is a powerful concept for
developing large collections of structurally diverse small mole-
cules, with the aim to explore larger portions of the chemical space
in drug discovery issues and in the investigation of biological path-
ways. The principles of DOS span from the concept of generating
structurally diverse compounds from a divergent approach con-
sisting in a complexity-generating reaction followed by cyclization
steps and appendage diversity, to the development of different cyc-
lic structures through the build/couple/pair approach.2 Also,
among the synthetic strategies to produce new chemical entities,
cascade, multicomponent, and multistep one-pot reactions have
gained wide acceptance because they increase synthetic efficiency
by decreasing the number of laboratory operations required and
the quantities of chemicals and solvents used.3 Thus, these reac-
tions can facilitate ecologically and economically favorable synthe-
ses. Recently, we turned our attention to the chemistry of
morpholines,4 as this heterocycle represents a common motif in
medicinal chemistry, being found in several bioactive molecules,
such as TACE, MMP, and TNF inhibitors.5 Among the privileged het-
erocycles, diketopiperazines (DKPs) have been found to possess
important biological properties, such as antitumor, antimicrobial,
and antiviral activities.6 Also, piperazines and 2-oxopiperazines
have been widely recognized as ‘privileged scaffolds’ in medicinal
chemistry, due to their presence as structural elements in a vast ar-
ray of natural products and biologically active compounds.7
We envisioned the possibility of using morpholine-based het-
erocycles to achieve a skeletal diversity through the manipulation
of the couple/pair approach. Specifically, the strategic approach
was conceived to access different scaffolds by the combination of
morpholine acetals with some
a-amino acids via a one-pot process
or a stepwise route (Scheme 1).
The modulation of the synthetic process using identical cou-
pling partners proved to give two different bicyclic structures as
a consequence of different mechanisms involved in the three-steps
routes.
Morpholine derivative 2 was achieved from O-protected threo-
nine and dimethoxyacetaldehyde as a separable mixture of diaste-
reomers, as reported.4b Interestingly, the reaction of unprotected
threonine methyl ester with phenacyl bromide in N-methylpyrroli-
done (NMP), followed by cyclization in acidic methanol gave access
to phenyl-substituted morpholine compound
4 as a single
stereoisomer in 36% overall yield (Scheme 2). Diagnostic NOE cor-
relation between the methoxy group at C-6 and H-2 allowed the
R1
O
N
R1
MeO
R1
O
N
O
one-pot
CO2Me
stepwise
CO2Me
O
R3
N
N
H
N
O
R3
O
R2
R1=R3=H
couple
R2
R2
cyclize to
scaffold A
Cl
cyclize to
scaffold B
O
A
B
N
R3
Fmoc
⇑
Corresponding author. Tel.: +39 055 4573507; fax: +39 055 4573531.
E-mail address: andrea.trabocchi@unifi.it (A. Trabocchi).
Scheme 1. Skeletal diversity through a couple-cyclize approach.
0040-4039/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2010.09.103

L. Ciofi et al. / Tetrahedron Letters 51 (2010) 6282–6285
Fmoc-aa-Cl
6283
MeO
O
HO
R1
O
N
ref. 4b
2,6-lutidine
CH2Cl2
pTSA
toluene
2h, reflux
R1
30%Et2NH
2h, r.t.
O
N
H
2
CO2Me
O
H2N
CO2Me
72%
MeO
2h, 60 °C
1
N
N
H
CO2Me
O
R3
3
1
2
R2
5-12
PhCOCH2Br
DIPEA, NMP
rt, 6h
2: R1=H
4: R1=Ph
nOe
H
H+/MeOH
reflux, 4.5h
MeO
HO
O
Figure 2. Sequential one-pot process to bicyclic diketopiperazines 5–12.
N
CO2Me
50%
N
H
CO2Me
H
O
bicyclic diketopiperazine by virtue of Fmoc-deprotection and con-
comitant intramolecular cyclization of the free amine to the ester
carbonyl group. This process proved to be effective for a number
of amino acids (Table 1),9 though phenylalanine and leucine
showed reduced yields, possibly due to the lowered stability of
the corresponding precursors in the process. Particularly effective
was the reaction with proline derivatives, giving the highest yields
in the overall three-step process using both morpholines 2 and 4.
The stepwise process10 consisted of an acid–base workup after
the coupling step, followed by treatment of the resulting adduct
in refluxing toluene (0.2 M) and in the presence of 1 equiv of pTSA
(Fig. 3). This protocol produced a different reaction outcome as a
consequence of a different mechanism taking part during the sec-
ond step of the process, giving bicyclic 2-oxopiperazines with
3
4
Scheme 2. Synthesis of morpholine ester scaffolds.
assignment of the C-6 absolute configuration, as shown in Scheme
2 and Figure 1.
Bicyclic compounds containing both the 1,4-dihydrooxazine
and the diketopiperazine nuclei were obtained through a sequen-
tial one-pot route embracing the three steps (Fig. 2). Specifically,
the process consisted of coupling of Fmoc-protected a-amino acyl
chlorides with morpholine derivatives 2 or 4, followed by acid-
mediated double bond formation to give the 1,4-dihydro-oxazine
nucleus and final Fmoc-deprotection with concomitant cyclization
to give the diketopiperazine cycle. This process was conceived by
applying a sequence of base-, acid-, and again base-mediated reac-
tions, all carried out in one-pot. Thus, the coupling of the Fmoc-
amino acid residue to the morpholine acetal was achieved by using
the corresponding Fmoc-amino acid chloride and 2 equiv of 2,6-lu-
tidine as base, as described by Carpino et al.8 The use of standard
COOH activators proved to be less efficient than the acyl chlorides
in the coupling reaction. After completion of the reaction, as judged
by TLC, 5 equiv of p-toluenesulfonic acid were added, and the mix-
ture was diluted with toluene to allow for the generation of the
intermediate 1,4-dihydroxazine ring by the azeotropical elimina-
tion of methanol. Such an amount of pTSA was assessed as the low-
est to achieve complete conversion to the oxazine intermediate.
Final treatment with an excess of diethylamine gave the final
Table 1
Sequential one-pot process to bicyclic diketopiperazines 5–12
Compd
Amino acid
R1
R2
R3
H
Yield (%)
5
6
Ph
Ph
H
CH(CH3)2
(CH2)3
32
92
76
69
48
77
34
15
L
L
L
-Val
-Pro
-Pro
7
(CH2)3
8
H
(CH2)3
D
-Pro
-(Bn)Ser
-Val
9
H
CH2OBn
CH(CH3)2
CH2Ph
H
H
H
H
L
10
11
12
H
D
H
L
L
-Phe
-Leu
H
CH2CH(CH3)2
Figure 1. Diagnostic NOE peaks between the irradiated proton H-2 and the methoxy group at C-6 of compound 4.

6284
L. Ciofi et al. / Tetrahedron Letters 51 (2010) 6282–6285
O
acid-base pTSA
work-up toluene
Fmoc-
removal
MeO
O
aa-coupling
N
CO2Me
HN
R1
1
2
3
N
H
CO2Me
O
R2
2
13-18
Figure 3. Stepwise process to bicyclic 2-oxopiperazines 13–18.
complete diastereoselectivity. This result was achieved by the re-
moval of 2,6-lutidine and its salts from the reaction mixture and
by the use of fixed amounts of pTSA and toluene. Adduct I
(Scheme 3), after protonation, is thought to undergo an intramo-
lecular attack by the protected nitrogen atom to the oxonium moi-
ety (structure II), followed by ring-opening of the morpholine ring
to the iminium III. This species isomerizes by a deprotonation–pro-
tonation process to the shifted iminium intermediate V, following
final cyclization to give the Fmoc-protected bicyclic 2-oxopiper-
azine VI.
According to this mechanism, the reaction of 2 with Fmoc-Pro-
Cl under these conditions did not proceed to the bicyclic 2-oxopip-
erazine scaffold but gave the corresponding bicyclic diketopipera-
zine after Fmoc-deprotection (Table 2, compd 7).
Moreover, morpholine derivative 4, bearing a phenyl group at
position 6 did not give the corresponding bicyclic 2-oxopiperazine,
due to the altered reactivity at the benzylic position which did not
allow for the rearrangement as described in Scheme 3.
Figure 4. NOE correlation for compound 13 and X-ray structure of 16.
NOE experiments on compound 13 were carried out to establish
the correct stereochemistry of the bicyclic 2-oxopiperazine scaf-
fold, as outlined in Figure 4. In particular, key NOE correlations be-
tween H-8a and H-2 of 13 unequivocably assessed the methylenic
group to be oriented in trans with respect to the carbomethoxy
group. This was in agreement with crystallographic data obtained
for compound 16,11 showing the predicted stereochemical assign-
ment of the newly-formed stereocenter and showing the six-mem-
bered ring in a boat-like conformation.
The herein reported new bicyclic scaffolds are particularly sui-
ted for peptidomimetic chemistry as dipeptide isosteres, and
appendage diversity may be achieved by using the chemistry at
the double bond for scaffold B of Figure 1, as already reported,4b
or applying scaffold A in peptide chemistry by virtue of the pres-
ence of carboxy and amino groups.
In conclusion, the process involving morpholine acetals and
suitable Fmoc-amino acid derivatives leads to two different bicy-
clic scaffolds depending on the reaction mode. Specifically, by car-
rying out the three-step process in one-pot with increasing
amounts of alternated base–acid–base reactants, the bicyclic dike-
topiperazine is formed preferentially, whereas the stepwise route,
by removing 2,6-lutidine and using the same reagents, leads to the
formation of a different bicyclic skeleton containing the 2-oxopip-
erazine ring, as a consequence of ring opening of the morpholine
nucleus. The concept of obtaining skeletal diversity by using same
reagents in a different manner may provide new efficient ways to
expand the access to chemical diversity by modulating both the re-
agents and the process. Application of these scaffolds in the gener-
ation of compound libraries through appendage diversity will be
reported in due course.
H
O
N
O
O
N
O
O
N
H+
- MeOH
CO2Me
CO2Me
CO2Me
FmocHN
FmocHN
FmocHN
O
O
O
R
R
R
II
I
H
O
O
H
Fmoc
N
Fmoc
N
N
N
CO2Me
N
CO2Me
R
R
O
O
Fmoc
R
Fmoc
R
H+
- H+
N
OH
N
OH
N
O
CO2Me
- H+
O
CO2Me
III
IV
Fmoc
Fmoc
R
O
N
OH
N
N
N
R
CO2Me
O
CO2Me
O
VI
V
Acknowledgments
Scheme 3. Hypothesized mechanism for the formation of the 2-oxopiperazine ring.
Fondazione Roma, University of Florence and CINMPIS are
acknowledged for the financial support. Dr. Cristina Faggi is grate-
fully acknowledged for carrying out X-ray crystallographic
analyses.
Table 2
Stepwise process to 2-oxopiperazinones 13–18
Compd
R1
R2
Yield (%)
L
-Amino acid
13
14
15
16
17
18
7
Val
Ala
Leu
Phe
Phg
H
H
H
H
H
CH3
H
CH(CH3)2
CH3
CH2CH(CH3)2
CH2Ph
Ph
76
31
41
67
41
55
References and notes
1. (a) Schreiber, S. L. Science 2000, 287, 1964; (b) Burke, M. D.; Berger, E. M.;
Schreiber, S. L. Science 2003, 302, 613; (c) Burke, M. D.; Schreiber, S. L. Angew.
Chem., Int. Ed. 2004, 43, 46.
2. (a) Arya, P.; Joseph, R.; Gan, Z.; Rakic, B. Chem. Biol. 2005, 12, 163; (b) Shun, S.;
Acquilano, D. E.; Arumugasamy, J.; Beeler, A. B.; Eastwood, E. L.; Giguere, J. R.;
Lan, P.; Lei, X.; Min, G. K.; Yeager, A. R.; Zhou, Y.; Panek, J. S.; Porco, J. A., Jr. Org.
Lett. 2005, 7, 2751; (c) Chen, C.; Li, X.; Neumann, C. S.; Lo, M. M.-C.; Schreiber, S.
a-Me-Ala
CH3
–(CH2)3–
a
Pro
—
a
The corresponding bicyclic diketopiperazine was obtained after Fmoc-removal.

L. Ciofi et al. / Tetrahedron Letters 51 (2010) 6282–6285
6285
L. Angew. Chem., Int. Ed. 2005, 44, 2249; (d) Mitchell, J. M.; Shaw, J. T. Angew.
Chem., Int. Ed. 2006, 45, 1722; (e) Kumagai, N.; Muncipinto, G.; Schreiber, S. L.
Angew. Chem., Int. Ed. 2006, 45, 3635; (f) Chen, Y.; Porco, J. A., Jr.; Panek, J. S. Org.
Lett. 2007, 9, 1529; (g) Thomas, G. L.; Spandl, R. J.; Glansdorp, F. G.; Welch, M.;
Bender, A.; Cockfield, J.; Lindsay, J. A.; Bryant, C.; Brown, D. F. J.; Loiseleur, O.;
Rudyk, H.; Ladlow, M.; Spring, D. R. Angew. Chem., Int. Ed. 2008, 47, 2808.
3. (a) Cameron, M.; Hoerrner, R. S.; McNamara, J. M.; Figus, M.; Thomas, S. Org.
Process Res. Dev. 2006, 10, 149; (b) Löfberg, C.; Grigg, R.; Keep, A.; Derrick, A.;
Sridharan, V.; Kilner, C. Chem. Commun. 2006, 5000; (c) Wang, C.-C.; Lee, J.-C.;
Luo, S.-Y.; Kulkarni, S. S.; Huang, Y.-W.; Lee, C.-C.; Chang, K.-L.; Hung, S.-C.
Nature 2007, 446, 896; (d) Peng, J.; Jiang, D.; Lin, W.; Chen, Y. Org. Biomol. Chem.
2007, 5, 1391; (e) Kammerer, C.; Prestat, G.; Gaillard, T.; Madec, D.; Poli, G. Org.
Lett. 2008, 10, 405; (f) Sirasani, G.; Andrade, R. B. Org. Lett. 2009, 11, 2085; (g)
Merkul, E.; Boersch, C.; Frank, W.; Müller, T. J. J. Org. Lett. 2009, 11, 2269; (h)
Werner, S.; Nielsen, S. D.; Wipf, P.; Turner, D. M.; Chambers, P. G.; Geib, S. J.;
Curran, D. P.; Zhang, W. J. Comb. Chem. 2009, 11, 452; (i) Rolfe, A.; Young, K.;
Volp, K.; Schoenen, F.; Neuenswander, B.; Lushington, G. H.; Hanson, P. R. J.
Comb. Chem. 2009, 11, 732; (j) Cao, C. P.; Sun, X.-L.; Zhu, B.-H.; Shen, Q.; Xie, Z.;
Tang, Y. Org. Lett. 2009, 11, 3048; (k) Pokhodylo, N. T.; Matiychuk, V. S.;
Obushak, M. D. J. Comb. Chem. 2009, 11, 481.
4. (a) Sladojevich, F.; Trabocchi, A.; Guarna, A. J. Org. Chem. 2007, 72, 4254; (b)
Sladojevich, F.; Trabocchi, A.; Guarna, A. Org. Biomol. Chem. 2008, 6, 3328; (c)
Lalli, C.; Trabocchi, A.; Sladojevich, F.; Menchi, G.; Guarna, A. Chem. Eur. J. 2009,
15, 7871; (d) Trabocchi, A.; Sladojevich, F.; Guarna, A. Chirality 2009, 21, 584;
(e) Sladojevich, F.; Guarna, A.; Trabocchi, A. Org. Biomol. Chem. 2010, 7, 916.
5. (a) Audouze, K.; Østergaard Nielsen, E.; Peters, D. J. Med. Chem. 2004, 47, 3089;
(b) Levin, J. I.; Chen, J. M.; Laakso, L. M.; Du, M.; Du, X.; Venkatesan, A. M.;
Sandanayaka, V.; Zask, A.; Xu, J.; Xu, W.; Zhang, Y.; Skotnicki, J. S. Bioorg. Med.
Chem. Lett. 2005, 15, 4345; (c) Xu, W.; Gray, D. L.; Glase, S. A.; Barta, N. S. Bioorg.
Med. Chem. Lett. 2008, 18, 5550; (d) Alexander, R.; Balasundaram, A.; Batchelor,
M.; Brookings, D.; Crépy, K.; Crabbe, T.; Deltent, M. F.; Driessens, F.; Gill, A.;
Harris, S.; Hutchinson, G.; Kulisa, C.; Merriman, M.; Mistry, P.; Parton, T.;
Turner, J.; Whitcombe, I.; Wright, S. Bioorg. Med. Chem. Lett. 2008, 18, 4316; (e)
Josien, H.; Bara, T.; Rajagopalan, M.; Clader, J. W.; Greenlee, W. J.; Favreau, L.;
Hyde, L. A.; Nomeir, A. A.; Parker, E. M.; Song, L.; Zhang, L.; Zhang, Q. Bioorg.
Med. Chem. Lett. 2009, 19, 6032; (f) Zask, A.; Kaplan, J.; Verheijen, J. C.; Richard,
D. J.; Curran, K.; Brooijmans, N.; Bennett, E. M.; Toral-Barza, L.; Hollander, I.;
Ayral-Kaloustian, S.; Yu, K. J. Med. Chem. 2009, 52, 7942.
G. H.; Stark, M. J. R.; Eggleston, I. M.; Van Aalten, D. M. F. J. Med. Chem. 2004, 47,
5713; (f) Abraham, W.-R. Drug Des. Rev. 2005, 2, 13; (g) Nicholson, B.; Lloyd, G.
K.; Miller, B. R.; Palladino, M. A.; Kiso, Y.; Hayashi, Y.; Neuteboom, S. T. C.
Anticancer Drugs 2006, 17, 25.
7. For a recent review on 2-oxopiperazines, see: De Risi, C.; Pelà, M.; Pollini, G. P.;
Trapella, C.; Zanirato, V. Tetrahedron: Asymmetry 2010, 21, 255.
8. Carpino, L. A.; Cohen, B. J.; Stephens, K. E., Jr.; Sadat-Aalaee, S. Y.; Tien, J. H.;
Langridge, D. C. J. Org. Chem. 1986, 51, 373.
9. General ‘one-pot’ procedure B: morpholine acetal 2 or 4 (1 equiv) was dissolved
in toluene (10 mL/mmol), then 2,6-lutidine (2 equiv) and Fmoc-aa-Cl (1 equiv)
were sequentially added. The reaction mixture was brought to 60 °C and stirred
for 2 h, then allowed to return at rt. Additional toluene (5 mL/mmol) and p-
toluenesulfonic acid monohydrate (5 equiv) were added, then the mixture was
placed in
a single-necked round-bottomed flask equipped with a reflux
condenser and a dropping funnel containing 4 Å molecular sieves and it was
refluxed for 2 h. The reaction mixture was brought back at rt and 30%
diethylamine solution in CH3CN (5 mL/mmol) was added. The reaction mixture
was stirred for 2 h at rt, then diluted with EtOAc (40 mL/mmol), washed with
5% NaHCO3 and brine. The organic layers were dried over anhydrous Na2SO4,
filtered and evaporated. A dark brown oil was obtained and purified by flash
chromatography (EtOAc–petroleum ether 2:1), giving the title 2,5-
diketopiperazine compounds as orange-yellow oils (for R = H) or pale yellow
solids (for R = Ph).
10. General ‘stepwise’ procedure A: morpholine acetal 2 (1 equiv) was dissolved in
anhydrous CH2Cl2 (4 mL/mmol), then 2,6-lutidine (2 equiv) and Fmoc-aa-Cl
(1 equiv) were sequentially added. The reaction mixture was brought to 60 °C
and stirred for 2 h under a nitrogen atmosphere. The reaction mixture was then
diluted with CH2Cl2 and sequentially washed with 5% HCl, 5% NaHCO3 and
brine. The organic layers were dried over Na2SO4, filtered and evaporated to
give a brownish foam. The crude product was then dissolved in toluene (5 mL/
mmol) and p-toluenesulfonic acid monohydrate (1 equiv) was added. The
reaction mixture was placed in
a
single-necked round-bottomed flask
dropping funnel containing 4 Å
equipped with reflux condenser and
a
a
molecular sieves and refluxed for 2 h, then it was allowed to return to rt. EtOAc
was added, and the organic solution was washed with 5% NaHCO3 and brine.
The organic layers were dried over anhydrous Na2SO4, filtered and evaporated
to give a dark brown oil. The crude product was dissolved in 30% diethylamine
in CH3CN (5 mL/mmol) and allowed to react for 2 h at rt. The reaction mixture
was then evaporated to obtain a pale brown solid, which was purified by flash
chromatography (EtOAc–petroleum ether 3:1), to give the title bicyclic 2-
oxopiperazine compounds as dark orange oils.
6. (a) Kanoh, K.; Kohno, S.; Katada, J.; Takahashi, J.; Uno, I. J. Antibiot. 1999, 52,
134; (b) Wennemers, H.; Conza, M.; Nold, M.; Krattiger, P. Chem. Eur. J. 2001, 7,
3342; (c) Byun, H.-G.; Zhang, H.; Mochizuki, M.; Adachi, K.; Shizuri, Y.; Lee, W.-
J.; Kim, S.-K. J. Antibiot. 2003, 56, 102; (d) Fdhila, F.; Vázquez, V.; Sánchez, J. L.;
Riguera, R. J. Nat. Prod. 2003, 66, 1299; (e) Houston, D. R.; Synstad, B.; Eijsink, V.
11. CCDC 769053.