Tertiary-butoxycarbonyl (Boc) – A strategic group for N-protection/deprotection in the synthesis of various natural/unnatural N-unprotected aminoacid cyanomethyl esters

Article abstract of DOI:10.1016/j.tetlet.2018.10.041

A number of cyanomethyl esters of natural/unnatural aminoacids with un-protected amino functionality were synthesized because of their synthetic and medicinal importance. Critical N-Boc deprotection methods in the presence of labile (hydrolytic sensitivity) cyanomethyl functionality were screened thoroughly and it was found that readily available 4M HCl in 1,4-dioxane solution (2–4 equiv); acetonitrile, 0 °C, 2–4 h was a suitable condition. This condition was generalized and successfully applied to a variety of alkyl, alkynyl, aryl, heteroaryl, benzyl, azido, spiro amino acid cyanomethylesters irrespective of the nature of the amine (primary or secondary) and the distance between the amine and ester group to achieve final deprotected amino esters with high yield, and purity compared to other commonly known N-protecting groups (Cbz, Fmoc, Ac, Bn, Bz etc.). It was also demonstrated that N-Boc protected aminoacid cyanomethylesters are stable enough to carry out further functionalization compared to N-unprotected counterparts.

Full text of DOI:10.1016/j.tetlet.2018.10.041

Accepted Manuscript
Tertiary-butoxycarbonyl (Boc) - A Strategic Group for N-Protection/Deprotec-
tion in the Synthesis of Various Natural/Unnatural N-unprotected Aminoacid
Cyanomethyl Esters
Ananta Karmakar, Mushkin Basha, G.T. Venkatesh Babu, Murali Botlagunta,
Noormohamed Abdul Malik, Richard Rampulla, Arvind Mathur, Arun Kumar
Gupta
PII:
S0040-4039(18)31259-0
https://doi.org/10.1016/j.tetlet.2018.10.041
TETL 50351
DOI:
Reference:
Tetrahedron Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
4 September 2018
16 October 2018
22 October 2018
Please cite this article as: Karmakar, A., Basha, M., Babu, G.T.V., Botlagunta, M., Malik, N.A., Rampulla, R.,
Mathur, A., Gupta, A.K., Tertiary-butoxycarbonyl (Boc) - A Strategic Group for N-Protection/Deprotection in the
Synthesis of Various Natural/Unnatural N-unprotected Aminoacid Cyanomethyl Esters, Tetrahedron Letters (2018),
doi: https://doi.org/10.1016/j.tetlet.2018.10.041
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Tertiary-butoxycarbonyl (Boc) - A Strategic Group for N-
Leave this area blank for abstract info.
Protection/Deprotection in the Synthesis of Various
Natural/Unnatural N-unprotected Aminoacid Cyanomethyl
Esters
Ananta Karmakar, Mushkin Basha, Venkatesh Babu G. T, Murali Botlagunta, Noormohamed Abdul Malik, Richard
Rampulla, Arvind Mathur, Arun Kumar Gupta
4M HCl in dioxane (2-4 equiv),
O
O
CH3CN, 0 oC, 2-4 hr
R1
R1
HN
O
CN
O
CN
N
79 - 97%
R2
Boc
R2
HCl salt
R1 = Alkyl, Alkynyl, Aryl, Heteroaryl, Benzyl, Azido, Spiro
R2 = H, Me
Tetrahedron Letters
journal homepage: www.elsevier.com
Tertiary-butoxycarbonyl (Boc) - A Strategic Group for N-Protection/Deprotection in
the Synthesis of Various Natural/Unnatural N-unprotected Aminoacid Cyanomethyl
Esters
Ananta Karmakar a, Mushkin Basha a, Venkatesh Babu G. T a, Murali Botlagunta a, Noormohamed Abdul
Malik a, Richard Rampulla b, Arvind Mathur b, Arun Kumar Gupta *,a
a
Department of Discovery Synthesis, Biocon Bristol Myers Squibb Research Centre, Plot 2 & 3, Bommasandra Industrial Estate - Phase-IV, Bommasandra-
Jigani Link Road, Bengaluru, Karnataka 560099, India
b Department of Discovery Synthesis, Bristol-Myers Squibb PRI, P.O. Box 4000, Princeton, NJ 08543-4000, USA
* arunkumar.gupta@syngeneintl.com
ARTICLE INFO
ABSTRACT
Article history:
Received
Received in revised form
Accepted
A number of cyanomethyl esters of natural/unnatural aminoacids with un-protected amino
functionality were synthesized because of their synthetic and medicinal importance. Critical N-
Boc deprotection methods in the presence of labile (hydrolytic sensitivity) cyanomethyl
functionality were screened thoroughly and it was found that readily available 4M HCl in 1,4-
dioxane solution (2-4 equiv); acetonitrile, 0 °C, 2-4 hr was a suitable condition. This
condition was generalized and successfully applied to a variety of alkyl, alkynyl, aryl,
heteroaryl, benzyl, azido, spiro amino acid cyanomethylesters irrespective of the nature of the
amine (primary or secondary) and the distance between the amine and ester group to achieve
final deprotected amino esters with high yield, and purity compared to other commonly known
N-protecting groups (Cbz, Fmoc, Ac, Bn, Bz etc.). It was also demonstrated that N-Boc
protected aminoacid cyanomethylesters are stable enough to carry out further functionalization
compared to N-unprotected counterparts.
Available online
Keywords:
Cyanomethyl,
N-Boc,
Aminoacids,
Deprotection,
tRNA analogs,
aminoacylation
2009 Elsevier Ltd. All rights reserved.
1. Introduction
Aminoacid cyanomethyl esters are an important class of compounds due to their synthetic versatility and importance in medicinal
chemistry. They have been used extensively as aminoacylating agents in the synthesis of aminoacyl-tRNA analogs,1 which is the first
key step for incorporation of the amino acids into proteins (nonnatural mutagenesis). Currently, the aminoacylation is being carried out
by synthesizing an aminoacylated pdCpA unit, followed by its enzymatic ligation to a truncated tRNA.1d Cyanomethyl esters have also
been reported to undergo facile trans-esterification with various alcohols.2 In addition, they are being used in peptide chemistry,3

dendrimer chemistry,4 enzymatic resolution of amines,5 acylation of buckyball amino acids6 and as useful protection for carboxylic
acids.7 Shapiro et. al. reported diazoacetic acid cyanomethyl esters as potential building blocks to access various synthetic conversions.8
Loeffler et. al.9 examined aminoacid cyanomethyl esters as potent anti-tumor, anti-inflammatory9a and anti-neoplastic agents.9b
Literature reveals that aminoacid cyanomethyl esters are very popular among the synthetic community because of their vast utility.
However, because of its hydrolytic sensitivity, the cyanomethyl ester group was tagged as poor acylating agent as discussed by Murray
Goodman et al10a compared to other acid activators.1h,10 Synthetic transformations of N-protected aminoacid cyanomethyl esters at the
"cyanomethyl ester" group have been well established. On the other hand, aminoacid cyanomethyl esters in the presence of a free amino
group still remain a challenge in organic synthesis. In all the previous reports10,11 in this regard, removal of the N-protection was
achieved either with compromised yield10a or by using a complex reaction protocol11a or by using relatively less studied protection like
the N-furfuryloxycarbonyl group.10b Shiori Kariyuki and co-workers achieved the N-deprotection in good yields by passing dry HCl gas
in a diethyl ether solution of the substrate.11b However, dry HCl gas could be replaced12a by more handy and readily available anhydrous
HCl solutions and also diethylether is not known as very versatile to solubilize highly polar substrates, particularly nitrogen containing
heterocycles.12b In all these reports, crude cyanomethyl esters after N-deprotection were taken as such for further utilization, probably
due to the challenges in purification. In consequence, adequate analytical data for compound characterization are also limited. To the
best of our knowledge, a literature survey did not yield any report to conquer these issues viz. to achieve N-deprotection in excellent
yield (>90%) and with high purity (>95%) on a broad range of substrates, and also maintain the cyanomethyl ester intact. The potential
usefulness of aminoacid cyanomethyl esters and lack of a generalized protocol for synthesis of this class of compounds led us to
examine and to establish a suitable protecting group with a simplified deprotection strategy. These achievements would certainly
expand the scope for further possibility of functionalization and molecular structural modification for application in synthetic as well as
in medicinal chemistry.
Herein, we report (a) N-Boc as a strategic protection, which was demonstrated by further functionalization and (b) a simple,
economical and efficient N-Boc deprotection protocol from the corresponding aminoacid cyanomethyl esters to accomplish above
mentioned goals. In our experience, handling of aminoacid cyanomethyl esters with an unprotected amino group compared to its N-
protected analogs is quite challenging due to the relatively fast nitrile hydration to the corresponding primary amides as well as
hydrolysis of the esters to the carboxylic acid. Additionally, in our own experience, purification of cyanomethyl aminoacid esters
containing an unprotected amino group was found to be highly challenging by column chromatography, preparative HPLC (normal or
reverse phase) or Supercritical Fluid Chromatography (SFC). In all the above mentioned purification attempts, increasing amount of
glycoamide 3a formation (20-60%) was observed.
2. Result and discussion
In search of an appropriate N-protection, a series of different common N-protected derivatives of (±)-phenylalanine cyanomethyl
esters (1a-1f) were synthesized and were subjected under regular deprotection conditions. Most of the reactions under each of these
conditions resulted in a mixture of several possible side products (Table 1) as indicated by LCMS monitoring.
Table 1. Deprotection of different N-protected phenyl-alaninesa
O
NH2
O
CONH2
O
CN
O
O
O
CN
NH2
Reaction
3a
2a
conditions
O
HN
O
R1
OH
R2
(±) 1a-1f
NH2
HN
4a
R1
5
a
Entry
Substrate
Condition
4M HCl (in 1,4-
Dioxane), DCM, 3h
Pd/C, H2,
EtOAc:THF (5:1),
2h
Results
All the reactions were monitored by LCMS and the distribution of product
formation was based on the crude LCMS profile.
1a (11%), 2a (39%),
3a (49%)
1
1a; (R1 = Boc)
Deprotection of N-Bn (1b, entry 2) or N-Cbz (1f, entry 6) under
hydrogenation conditions (1 atm, room temperature) resulted in a
mixture of compounds with almost no trace of either the desired
product or un-reacted starting material. On the other hand, N-Cbz
deprotection (entry 7) using Pd/C in combination with triethylsilane
produced a mixture of 41% of the parent phenylalanine (4a) and
36% of the N-Cbz phenylalanine (5f). Similarly N-Fmoc (1e, entry
5) deprotection using piperidine in dichloromethane resulted in 12%
phenylalanine together with 36% of the piperidinyl amide of
phenylalanine (5e) as the deprotected amine. When N-Bz (1c, entry
3) was treated under acidic conditions, it produced no desired
product 2a but 30% nitrile hydrated amide compound (5c; R1 = Bz,
R2 = OCH2CONH2). In addition, 40% complete hydrolysis of
cyanomethyl ester was observed (R1 = Bz, R2 = OH) with no N-Bz
2
3
1b; (R1 = Bn)
1c; (R1 = Bz)
Reaction not clean
5c (R1 = Bz,
4M HCl (in 1,4-
Dioxane), 12h
R2 = OCH2CO NH2)
(30%), and (R1 =
Bz, R2 = OH) (40%)
2a (11%), reaction
not clean
4
5
1d; (R1 = Ac)
1N HCl, MeOH, 2h
4a (12%), 5e (R1 =
H, R2 = Piperidine)
(36%)
Piperidine, DCM, rt,
1.5h
1e; (R1 = Fmoc)
Pd/C, EtOAc, H2, 1
atm, rt, 1.5h
Pd/C, Et3SiH,
1f (5%), reaction not
clean
6
7
1f; (R1 = Cbz)
1f; (R1 = Cbz)
4a (41%), 5f (R2 =
OH) (36%)
MeOH, rt, 1.5h
cleavage. However, acidic treatment of N-Ac derivative (1d, entry 4) and N-Boc compound (1a, entry 1) demonstrated mild hope with
formation of 11% and 39% of the desired product (2a), respectively. Notably, N-Boc deprotection produced 49% of the nitrile
hydrolyzed amide (3a) as the major product. Literature also reveals these observations as analogous compounds with cyanomethyl ester
functionality under acidic conditions (HCl or HBr/AcOH) promote hydration of the nitrile group to yield glycoamide esters.13

Table 2. N-deprotection of (±)-cyanomethyl (tert-butoxy carbonyl)phenylalaninate (1a)
O
O
CN
O
CN
Reaction
NH2
O
conditions
O
O
NH2
O
HN
NH2
Boc
(±)-1a
2a
3a
a 4M HCl in 1,4-dioxane was purchased commercially.
Entry
Acid (2 eq)a
Solvent / Time
Results
b Acids were added to a ice-cooled (0 °C) solution of 1a in respective solvents
and the reaction mixture was brought to 10-15 °C over a period of 3h.
c The % of formation of 1a, 2a & 3a were monitored by LCMS.
1
2
TFA
TFA
HBr (33 wt% in
AcOH)
TBAF
4M HCl (in 1,4-
Dioxane),
4M HCl (in 1,4-
Dioxane),
4M HCl (in 1,4-
Dioxane),
4M HCl (in 1,4-
Dioxane),
CH2Cl2 / 3h
1,4-dioxane / 3h
Reaction not clean
2a (6%), 3a (18%)
3
4
5
None / 2h
THF / 1h
3a (68%)
We then studied the deprotection of the N-Boc of cyanomethyl
(tert-butoxycarbonyl) phenylalaninate (1a) to achieve best results
under different commonly used reaction conditions, as in Table 2.
The reaction was not clean enough under TFA (2.5 equiv), CH2Cl2
condition (entry 1), whereas changing the solvent to 1,4-dioxane, it
produced only 6% of the desired product 2a along with formation of
18% of the hydrated amide 3a (entry 2). HBr (33 wt% in AcOH)
also failed to generate the desired compound, and yielded only
amide 3a (entry 3). Using TBAF, deprotection was found to produce
a complex mixture (entry 4). HCl, however, appeared to be a more
No desired product
1a (11%), 2a (39%),
3a (49%)
CH2Cl2 / 2h
6
7
8
9
MeOH / 2h
2a (9%), 3a (79%)
1a (23%), 2a (28%),
3a (48%)
1,4-dioxane / 2h
CH3CN / 3h
CH3CN / 12h
2a > 95%
4M HCl (in 1,4-
Dioxane),
2a (40%), 3a (54%)
suitable choice in terms of cleanliness of the reaction (entry 5 to 8). Using 2.5 equiv of HCl (4M solution in 1,4-dioxane) in
combination with solvents like CH2Cl2, MeOH and 1,4-dioxane produced the desired product in 39%, 9% and 28%, respectively (entry
5 to 7) along with a significant amount of the undesired amide (3a). However, to our surprise, use of acetonitrile as solvent under the
same reaction conditions (entry 8), resulted in exclusive formation of >95% of 2a within 3 hours with negligible amount (<2%) of 3a
observed. Extension of the reaction time to 12h, results in a significant amount (54%) of amide 3a (entry 9). Being mild Lewis basic in
character,14 acetonitrile might be dominating as H+ receptor and thus controlling the protonation of CN group of cyanomethyl ester to
suppress hydrolysis to amide 3a and to yield >95% of 2a within stipulated reaction time (3 hr; entry 8). However, extension of reaction
time under the same condition slowly enriches amide 3a (54% after 12 hr; entry 9). In case of methanol, formation of amide 3a is high
(79%; entry 6) as polar protic solvents are known to promote hydrolysis under acidic condition. Surprisingly, when the reaction was
performed using DCM, a significant amount of 3a (49%; entry 5) was observed. Probably, the hydrophobic nature of DCM permits
both residual moisture and HCl to interact with the CN group and hydrolyze the duly formed 2a (HCl salt) to the corresponding amide
3a.
In order to check the scope of this above reaction condition, a variety of N-Boc protected aminoacid cyanomethyl esters were
synthesized (1a, 1g-1z') as in Table 3. Synthesis of N-Boc aminoacid cyanomethyl esters (1a, 1g-1x) were performed following the
route-A protocol as shown in scheme 1. N-methyl analogues (1y-1z') were synthesized through route-B (Scheme 1). For the synthesis
of starting N-Boc cyanomethyl ester 1, mainly two different routes were utilized. Route A was applied for free -NH2 compounds (Table
2, entry 1-19). An excess equivalent of NaOH (2.2 equiv) was used during Boc protection of aminoacid (AA) and either direct
concentration or aqueous workup (after neutralization with 1.5N HCl) of the reaction solution resulted in white gummy solids of N-Boc
aminoacid sodium salt (6) or N-Boc aminoacid (6a) respectively. Both the intermediate 6 and 6a were used as such in the next
esterification step with chloroacetonitrile, triethylamine in DMF to afford a very good yield (80-90% isolated yield) of substrate 1 after
column purification.
(Boc)2O (1.2 eq),
Chloroacetonitrile (1.5 eq),
O
CN
O
O
NaOH (2.2 eq),
tBuOH:H2O (2:1)
TEA (1.2 eq),
DMF
R1
R1
R1
O
OR
NHBoc
6;
OH
Route A
NHBoc
80-90% after 2 steps
NH2
AA
1
R = Na
6a;
R = H
Route B
(Boc)2O (1.2 eq),
NaOH (2.2 eq),
tBuOH:H2O (2:1)
95-99%
O
CN
O
(1)
MeI (2.5 eq),
NaH (3 eq), DMF
Chloroacetonitrile (1.5 eq),
DIPEA (1.2 eq), THF
O
R1
R1
R1
O
OH
OH
(2)
NaOH (1.5 eq)
80-90%
NBoc
NBoc
NHBoc
6'
1'
THF:H2O (3:1)
7
70-80%
Scheme 1. General Scheme for Synthesis of N-Boc aminoacid cyanomethyl esters
Route B was used mostly for N-methylated compounds. In these cases intermediate 6' was treated with MeI, NaH and DMF to
furnish N-methylation along with methyl esterification of the carboxylic acid. Hydrolysis of the methyl ester generated N-methyl-N-Boc
aminoacid 7 followed by cyanomethyl esterfication to generate N-methyl, N-Boc aminoacid cyanomethyl ester 1'. It is worthy to
mention here that under these reaction conditions, no epimerization was observed for optically active substrates.

Table 3. N-Boc deprotection of Substrate 1a, 1g - 1z'
O
O
R1
HN
4M HCl in dioxane (2.5 eq),
R1
O
CN
CH3CN, 0 oC, 2-4 hr
O
CN
N
R2
HCl salt
Boc
R2
1a, 1g-1z'
2a, 2g-2z'

Product
(as HCl salt)
Yielda a Isolated yields
Entry Substrate
(%)
b Isolated as corresponding phenol
c Reaction time is 2hr only.
O
O
All the synthesized N-Boc aminoacid cyanomethyl esters (1a, 1g-
1z') were subjected to Boc deprotection using the optimized
condition as in Table 3 to give excellent yields with high purity (95-
99% by HPLC).15 Here a variety of natural/unnatural amino acids
namely alkyl, alkynyl, aryl, benzyl, heteroaryl, azido, and spiro
compounds were tested. In a few limited cases (entry 7, 8, 11)
formation of the hydrated amide was observed in negligible amount
i.e. in the range of 1-5%. A diversity of functional groups were
found tolerable and showed no impact towards the stability of the
corresponding cyanomethyl esters. Functional groups like alkyne
(entry 2, 19), azide (entry 9), heteroaryl (entry 7, 8, 12), thioether
(entry 17), cyano (entry 13), biaryl (entry 5) and hydroxy (entry 14,
15) were found stable enough to achieve the deprotection of N-Boc
with a very high level of purity. Removal of two N-Boc groups
(entry 8) was also successful in the presence of the cyanomethyl
ester. Fluoro-tyrosines, because of their biological importance16
were also taken under consideration (entry 14, 15) and resulted in
93% and 90% yields, respectively. The O-tBu functional group was
found to be not stable under these reaction conditions, and as
expected, it undergoes cleavage to yield the corresponding phenolic
derivative (entry 6).
O
CN
O
O
CN
1
94
HN
NH2
Boc
(±)-2a
(±)-1a
CN
O
CN
O
O
2
3
4
97
90
89
NHBoc
NH2
O
O
(±)-2g
(±)-1g
O
O
O
CN
O
CN
NHBoc
NH2
(S)-1h
(S)-2h
O
O
O
CN
O
CN
NHBoc
NH2
(±)-2i
(±)-1i
Br
Br
O
O
O
CN
O
O
CN
(S)-2j
5
6
7
8
96
NHBoc
NH2
O
Ph
Ph
(S)-1j
O
92b
79c
80
CN
CN
O
NH2
NHBoc
(S)-1k
(S)-2k
HO
O
O
O
N
N
O
CN
(S)-1l
O
O
CN
NHBoc
NH2
H2N
(S)-2l
O
BocHN
N
N
To understand the impact and significance of N-Boc protection
for this set of compounds, further derivatization was attempted on
N-Boc protected analogue 1g and 1n. Functionalization on the
terminal propargyl group was performed using either a Sonogashira
reaction17 with 4-bromotoluene, or a [3+2] Click cycloaddition18
between 1g and 1n (Scheme 2). In parallel, similar chemistry were
attempted with their deprotected compounds, 2g and 2n. It was
found that the reactions provided good yields of the desired
compound 8 (58% isolated yield for Sonogashira coupling) and 10
(60% isolated yield for [3+2] cycloaddition). When both of the
products were treated with our optimized deprotection condition,
excellent results were obtained to provide compound 9 (92% yield)
and compound 11 (90% yield), respectively. In contrast, when the
deprotected compounds (2g and 2n) were subjected under exactly
the same reaction conditions for the Sonogashira and the [3+2] click
reaction in an attempt to produce compounds 9 and 11 directly, both
reactions provided a complex mixture. Conversion of 10 to 11 is
also important as the reaction demonstrates that two cyanomethyl
ester groups are maintained intact during deprotection of two N-Boc
groups.
O
O
BocN
HN
CN
(S)-1m
CN
(S)-2m
O
O
O
CN
O
CN
9
94
N3
NH2
N3
NHBoc
(±)-1n
(±)-2n
O
O
BocHN
CN
N
H2N
CN
N
10
11
93
89
O
O
1o
2o
O
O
BocN
S
HN
S
O
O
1p
2p
O
O
O
CN
(±)-1q
O
CN
12
13
14
15
16
92
96
93
90
87
HN
NH2
Boc
(±)-2q
O
O
O
CN
O
O
CN
CN
NHBoc
(S)-1r
NH2
(S)-2r
NC
NC
O
O
F
F
O
CN
NH2
(S)-2s
O
NHBoc
(S)-1s
HO
HO
F
F
F
F
O
F
F
3. Conclusion
O
CN
O
CN
CN
NH2
NHBoc
(S)-1t
HO
HO
(S)-2t
In summary, we have demonstrated N-Boc as a suitable
protecting group for aminoacid cyanomethyl esters, and have
identified a simple, efficient Boc deprotection protocol for these
compounds which was optimized and successfully demonstrated,
where other well recognized N-protections failed to provide the
desired products. This protocol provides analogs in high purity by
maintaining the integrity of the -cyano as well as the cyanomethyl
ester functionality. We believe these findings will certainly unlock
the scope for further possibility of functionalization and molecular
structural modification for application in synthetic as well as
medicinal chemistry.
F
F
O
O
O
CN
O
NHBoc
(S)-1u
NH2
F
F
(S)-2u
O
O
S
S
O
CN
O
CN
17
18
90
92
NHBoc
NH2
O
(S)-1v
(S)-2v
O
BocHN
O
CN
H2N
O
CN
1w
2w
NHBoc
O
NH2
CN
O
CN
19
20
21
89
91
96
O
O
O
(±)-2x
(±)-1x
CN
O
CN
BocN
N
H
O
N
O
2y
1y
O
O
O
CN
O
CN
HN
Boc
CH3
CH3
(S)-2z
(S)-1z
O
O
O
CN
O
CN
22
94
N
HN
HO
Boc
(S)-1z'
HO
(S)-2z'

(1) Sonogashira reaction:
O
Pd(PPh3)2Cl2,
CuI, DIPEA,
DMF, rt, 12h
I
O
O
N
NHBoc
O
O
N
+
NHBoc
(±)-1g
58%
(±)-8
O
CH3
I
4M HCl in dioxane,
CH3CN, 0 oC, 2 hr
92%
4M HCl in dioxane,
CH3CN, 0 oC, 2 hr
97%
H3C
O
Pd(PPh3)2Cl2,
CuI, DIPEA,
O
O
DMF, rt, 12h x
N
NH2.HCl
+
O
O
Complex
N
mixture
NH2.HCl
(±)-9
O
CH3
(±)-2g
H3C
O
Na-ascorbate,
CuSO4.5H2O
tBuOH:Water (1:1),
CN
rt, 12h
(2) Click [3+2] reaction:
O
O
O
N
NHBoc
O
O
N
N
BocHN
O
CN
O
N
NHBoc
N
BocHN
N3
60%
O
(±)-1g
(±)-1n
(±)-10
O
4M HCl in dioxane,
CH3CN, 0 oC, 2 hr
90%
4M HCl in dioxane,
CH3CN, 0 oC, 2 hr
97%
4M HCl in dioxane,
CH3CN, 0 oC, 2 hr
94%
O
Na-ascorbate,
CuSO4.5H2O
tBuOH:Water (1:1),
rt, 12h
O
O
O
N
NH2.HCl
O
CN
O
CN
O
N
N
ClH.H2N
O
NH2.HCl
N
x
ClH.H2N
N3
N
O
Complex
mixture
(±)-2g
(±)-11
(±)-2n
O
Scheme 2. Sonogashira and Click reaction with and without N-Boc protection
Acknowledgments
Authors are thankful to Discovery Analytical Department, Biocon Bristol Myers Squibb Research Centre (BBRC), Bangalore, India
for Analytical support and are very grateful to Dr. Jianqing Li and Dr. Michael Poss, Bristol Myers Squibb Company, USA for their
valuable suggestions and assistance.
References and notes
1.
(a) Wang, L., Schultz, P. Z., Angew. Chem. Int. Ed. 2005, 44, 34 (b) Fonvielle, M., Chemama, M., Re´gis Villet, R., Lecerf, M., Bouhss, A., Vale´ry,
J-M., Quelquejeu, M. E., Arthur, M., Nucleic Acids Research, 2009, 1-13 (c) Zhu, X., Scott, A., Nucleosides Nucleotides Nucleic Acids, 2001, 20, 197
(d) Ninomiya, K., Kurita, T., Hohsaka, T., Sisido, M., Chem. Commun., 2003, 17, 2242 (e) Murakami, H., Bonzagni, Suga, H., J. Am. Chem. Soc.
2002, 124, 6834 (f) Suga, H., Lohse, P. A., Szostak, J. W., J. Am. Chem. Soc., 1998, 120, 1151 (g) Murakami, H., Saito, H., Suga, H., Chem. & Biol.,
2003, 10, 655 (h) Suga, H., Hayashi, G., Terasaka, N., Phil. Trans. R. Soc. B, 2011, 366, 2959 (i) Jongkees, S. A. K., Caner, S., Tysoe, C., Brayer, G.
D., Withers, S. G., Suga, H., Cell. Chem. Biol., 2017, 24, 381
2.
(a) Greene, T. W.; Wuts, P. G.M. Protective Groups in Organic Synthesis, 3rd ed.; Wiley: New York, 1999; Chapter 7, pp 518-525 and references
cited therein. (b) Hennen, W. J.; Sweers, H. M.; Wang, Y. F.; Wong, C.-H. J. Org. Chem. 1988, 53, 4939. (c) Ellman, J.; Mendel, D.; Anthony-Cahill,
S.; Noren, C. J.; Schultz, P. G. Methods Enzymol. 1991, 202, 301. (d) Robertson, S. A.; Ellman, J. A.; Schultz, P. G., J. Am. Chem. Soc., 1991, 113,
2722. (e) Findlow, S.; Gaskin, P.; Harrison, P. A.; Lenton, J. R.; Penny, M.; Willis, C. L. J. Chem. Soc., Perkin Trans. 1, 1997, 5, 751
(a) Schwyzer, R., Iselin, B., Feurer, M., Helv. Chim. Acta, 1955, 38, 69 (b) Schwyzer, R., Feurer, M., Iselin, B., Kagi, H., Helv. Chim. Acta, 1955, 38,
80 (c) Schwyzer, R., Feurer, M., Iselin, B., Helv. Chim. Acta, 1955, 38, 83 (d) Schwyzer, R., Iselin, B., Rittel, W., Sieber, P., Helv. Chim. Acta, 1956,
39, 872. (e) West, J. B.; Scholten, J.; Stolowich, N. J.; Hogg, J. L.; Scott, A. I.; Wong, C.-H., J. Am. Chem. Soc., 1988, 110, 3709
(a) Bouillon,C., Tintaru, A., Monnier, V., Charles, L., Elever, Q., Peng, L., J. Org. Chem., 2010, 75, 8685 (b) Bouillon, C., Quéléver G., Peng, L., Tet.
Lett. 2009, 50, 4346
3.
4.
5.
6.
7.
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Takayama, S., Moree, W. J., Wong, C-H., Tet. Lett., 1996, 37, 6287
Strom, T. A., Barron, A. R., All Res. J. Nano, 2015, 1, 4.
Hugel, H. M., Bhaskar, K. V., Longmore, R. W., Synth. comm., 1992, 22, 693
Shapiro, E. A., Dyatkin, A. B., Nefedov, O. M., Bull. Russ. Acad. Sci. Div. Chem. Sci. (Engl. Transl.), 1992, 41, 272
(a) Loeffler, L. J., Sajadi, Z., Hall, I. H., Jnl. Med. Chem. 1977, 20, 1578 (b) Sajadi, Z., Almahmood, M., Loeffler, L. J., Hall, I. H., Jnl. Med. Chem.,
1979, 22, 1419
10. (a) Goodman, M., Stueben K. C., J. Am. Chem. Soc., 1959, 81, 3980 (b) Jeschkeit, H., Losse, G., Neubert. K, Chemische Berichte, 1966, 99, 2803
11. (a) West, J. B., Hennen, W. J., Lalonde, J. L., Bibbs, J. A., Zhong, Z., Meyer, E. F. Jr., Wong, C-H., J. Am. Chem. Soc., 1990, 112, 5313 (b) Kariyuki,
S., Takeo. I., Kojima, M., Takeyama, R., Tanada, M., Kojima, T., Iikura, H., Matsuo, A., Shiraishi, T., Emura, T., Nakano, K., Takano, K., Asou, K.,
Torizawa, T., Takano, R., Hisada, N., Murao, N., Ohta,A., Kimura, K., Yamagishi, Y., Kato, T. US 2015/0080549 A1, 2015. (c) Suga, H., Kourouklis,
D., Saito, H., Lee, N., Bonzagni, N. US 7001723 B1, 2006
12. (a) Coffey, D. S., Hawk, M. K. N., Pedersen, S. W., Ghera, S. J., Marler, P. G., Dodson, P. N., Lytle, M. L., Org. Proc. Res. Dev., 2004, 8, 945
(b)Kucharski, M., Glowacz-Czerwonka, D., Jnl.of Appl. Pol. Sci., 2002, 84, 2650
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14. Denmark, S. E., Beutner, G. L., Angew. Chem. Int. Ed., 2008, 47, 1560
15. General Procedure: To a stirred solution of N-Boc aminoacid cyanomethyl ester 1 (1 equiv) in acetonitrile (4 mL/equiv of 1) was added HCl (4M in
dioxane) (2 equiv) slowly at 0 °C under nitrogen atmosphere. The mixture was stirred for 2h. During this period, the reaction temperature was
maintained between 10-15 °C. In case of incomplete conversion, another 1-2 equiv of HCl (4M in dioxane) was added and stirring was continued with
continuous monitoring till complete consumption of 1. The reaction mixture was then concentrated at 30-35 °C under reduced pressure to provide a
gummy liquid. The gummy crude was dissolved in a minimum amount of acetonitrile, and to that solution was added excess diethylether to precipitate
out the desired product as white solids. In case of non-hygroscopic compound, the solids were filtered. Otherwise, the diethyl ether layer was decanted
off; the remaining solid suspension was dried under vacuum. Next, the solids were further washed with diethyl ether, and dried under vacuum to

produce the desired product 2 as a hydrochloride salt. [Removal of traces of hydrated amide 3: White solids thus obtained were stirred vigorously with
15% MeOH/diethyl ether solution for 15 min and filtered. This washing protocol should be repeated for 2-3 times to achieve highest purity (HPLC >
95%) of desired product 2]
16. Oyala, P. H., Ravichandran, K. R., Funk, M. A., Stucky, P.A., Stich, T. A., Drennan, C. L., Britt, R. D., Stubbe, J. A., J. Am. Chem. Soc., 2016, 138,
7951
17. Sonogashira, K.; Tohda, Y.; Hagihara, N. Tet. Lett. 1975, 16, 4467
18. Rostovtsev, V.V., Green, L. G., Fokin, V. V., Sharpless, K. B., Angew. Chem. Int. Ed., 2002, 41, 2596
Supplementary Material
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Highlights
Manuscript title: “Tertiary-butoxycarbonyl (Boc)-A Strategic Group for N-Protection/Deprotection
in the Synthesis of Various Natural/Unnatural N-unprotected Aminoacid Cyanomethyl Esters”
1. Extensively used in medicinal chemistry, as aminoacylating agents in the synthesis of
aminoacyl-tRNA analogs
2. Used in peptide, dendrimer, buckyball amino acid, protection for carboxylic acids chemistry
and resolution of amines
3. Achieving pure aminoacid cyanomethyl esters with an unprotected amine group remain a
challenge
4. Here in cyanomethyl esters N-deprotection were isolated and well characterised by adequate
analytical data
Graphical Abstract
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Tertiary-butoxycarbonyl (Boc) - A Strategic Group for N-
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Protection/Deprotection in the Synthesis of Various
Natural/Unnatural N-unprotected Aminoacid Cyanomethyl
Esters
Ananta Karmakar, Mushkin Basha, Venkatesh Babu G. T, Murali Botlagunta, Noormohamed Abdul Malik, Richard
Rampulla, Arvind Mathur, Arun Kumar Gupta
4M HCl in dioxane (2-4 equiv),
O
O
CH3CN, 0 oC, 2-4 hr
R1
R1
HN
O
CN
O
CN
N
79 - 97%
R2
Boc
R2
HCl salt
R1 = Alkyl, Alkynyl, Aryl, Heteroaryl, Benzyl, Azido, Spiro
R2 = H, Me
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