Accepted Manuscript Design and Synthesis of New Vancomycin Derivatives Wen Gu, Bei Chen, Min Ge PII: DOI: Reference:
S0960-894X(14)00329-1 http://dx.doi.org/10.1016/j.bmcl.2014.03.093 BMCL 21486
To appear in:
Bioorganic & Medicinal Chemistry Letters
Received Date: Revised Date: Accepted Date:
4 December 2013 23 March 2014 25 March 2014
Please cite this article as: Gu, W., Chen, B., Ge, M., Design and Synthesis of New Vancomycin Derivatives, Bioorganic & Medicinal Chemistry Letters (2014), doi: http://dx.doi.org/10.1016/j.bmcl.2014.03.093
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Design and Synthesis of New Vancomycin Derivatives Wen Gua, Bei Chena, Min Gea,b,* a
College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 210009, China b.
Acesys PharmaTech, Inc., Science and Technology Building 24B, 5 Xing Mo Fang Road, Nanjing, 210009, China
This is where the receipt/accepted dates will go; Received Month XX, 2000; Accepted Month XX, 2000 [BMCL RECEIPT]
Abstract—A set of vancomycin derivatives with lipid chain attached via a glyceric acid linker was designed and synthesized. A concise synthesis towards these derivatives was developed and the IC50s of these new lipoglycopeptides were tested. Some of them showed very potent activity against both vancomycin sensitive and resistant strains.
The glycopeptides antibiotics are the most important drugs in current use for the treatment of Gram-positive bacterial infections. They function through binding to the bacterial cell wall substrate DAla-D-Ala and thus inhibiting the transpeptidation step. In 1990s, vancomycin resistant enterococci (VREs) and vancomycin-resistant staphylococcus aureus (VRSA) emerged which posed a very serious public health problem. This led to new interests in the development of antibiotics of different class as well as new derivatives of the glycopeptides.
HO R 1 NH OH O OH Me O
Me
OH O O O R2 O O O
N H H
HN HO
O
H N O
HO
------------------------------* Corresponding author. Tel.: +86 025 83421757; fax: +86 025 83172563; e-mail: [email protected]
N H O
OH O
H N O
N H
H N Me
OH OH
vancomycin: Oritavancin:
Many different types of vancomycin derivatives were prepared and studied. The most successful finding is the discovery by Nagarajan et al that attaching lipid chain to the vancomycin carbohydrate portion led to significant potency boost towards both vancomycin sensitive and resistant strains.[1] These modifications eventually led to the development of a new glycopeptide antibiotic called oritavancin which is now close to FDA filing (Figure 1). Studies suggest that these new vancomycin derivatives with lipid chain attached (lipoglycopeptides) have dual mechanisms by inhibiting both transpeptidation and the transglycosylation steps of the cell wall biosynthesis.[2] The alycone portion binds the cell wall substrate and the lipid carbohydrate portion inhibits the transglycosylases at the same time. Interestingly, we notice that another transglycosylase inhibitor – moenomycin (Figure 1) also has a similar structure feature where a long lipid chain is attached to its carbohydrate portion via a glyceric acid linker. Kahne group has extensively studied the functions of the C55 lipid chain as well as the carbohydrate portion.[3] However, the function of this glyceric acid phosphate linker remains unknown.
Cl
NH2
C O
O
Cl
O HO HO O OH HO NH H3C O O HO OH HO
R1=H, R2=H R1=
Cl
H 2N HO
OH O
O
O
O CH 2 O OH O O HO NHAc NHAc O O
P
HO Me
NH 2 O Me O
CH 3 O NH 2 O
O
O
R2=
O OH
HO2C
Moenomycin Figure 1. Chemical structures of vancomycin, oritavancin and moenomycin.
During the development of the lipoglycopeptides, it was found that these derivatives have poorer solubility in water compared to vancomycin. In addition, the greasy chain caused unwanted ion-channel side effect. How to improve aqueous solubility while improving the potency is a challenging problem in this area. We have noticed the similarity between the lipoglycopeptides and moenomycin. It was interesting to understand the role of the glyceric acid-phosphate portion of moenomycin is. Here we designed a set of vancomycin derivatives with lipid chains attached to the carbohydrate portion via a similar glyceric acid linker. Our assumption is that an important structural feature “borrowed” from a transglycosylase inhibitor should
1
also be helpful to the transglycosylase inhibiting effect of the vancomycin carbohydrate portion. In addition, the added polarity of this acid linker should also help to lower the LogP, improve the solubility and reduce the unwanted ion channel side effect. On the other hand, studies on these analogs may also give us some hints of the role of this glyceric acid linker in moenomycin. A straightforward way for making these new derivatives is through the reductive-amination between ester 1 and vancomycin (Scheme 1). We tried a few methods to make this unique ester. At first, we converted serine into methyl 2-bromo-3hydroxypropanoate 2 through diazonium reaction and esterification. However, all attempts to displace the alfa-bromide with alkoxide only led to the decomposition of 2. We then tried the Kahne procedure and prepared the ester 5.[4] However, the final oxidation of the hydroxyl group failed completely with every oxidation reagent we tried, presumably due to the instability of the final product. Scheme 1a. Attempted syntheses of compound 1. OH O
a, b
O OMe
OMe
OH Br
NH2
OH OH OH
O
OH O
c, d, e
OR
2
OH OH OR
f, g
1
OH O OMe
OH OH OH 3
OR OH OH 4
OR 5
a
Reagents and conditions: (a) NaNO2, HBr; (b) MeOH, HCl; (c) PMB dimethoxy ketal, TsOH; (d) RBr, NaH; (e) AcOH, H2O; (f) NaIO4, THF, H2O; (g) NaClO2, NaH2PO4, H2O, 2-methyl-2-butene; then MeOH, HCl.
After lots of literature searching and experimentation, we found that the condensation of methyl 2-benzoxy-acetate with methyl formate can provided the sodium salt of desire product in one single step (entry 1, table 1).[5] The product is quite stable as potassium salt. This method can also be applied to other 2-alkoxy-acetates to give a series of 3-oxy propionates. Proton NMR indicated that these compounds are in their enolate form which makes them much more stable.
a,b R-OH
O RO
Entry
R=
1
benzyl
c
O-K+ O OMe
OMe
OR
Product
Yield[%]
OMe O
63
O 1a
+ -
KO
OMe 2
chlorobiphenyl methyl
O
Cl O
+ -
KO O
3
n-butyl
OMe 66
+K - O
O 1c O
4
n-hexyl
79
1b
OMe 55
+K- O
1d
O
a
Reagents and conditions: (a) chloroacetic acid, NaH, THF; (b) SOCl2, MeOH; (c) KOtBu, methyl formate, ether.
Next we studied the reductive-amination reaction between compounds 1a-1d and vancomycin. Following the known condition (DMF, NaBH3CN, 80℃)[1], we only obtained the enamine intermediate. Attempts to reduce this intermediate with various reducing agents all failed (entry 1, 2, 3, table 2). During the isolation of this intermediate, we noticed that it was less stable under acidic conditions. With this in mind, we adjusted the acidity of the reaction media. A 1:1 mixture of DMF and acetic acid turned out to be the best reaction solvent and high temperature (80 ℃) was also needed. Complete reduction of the enamine intermediate was achieved to give 6a (entry 4, table 2) [6]. Compounds 6b-6d were synthesized in similar fashion (entry 5-8, table 2). Thus, a concise synthesis of these vancomycin derivatives with lipid-glyceric linker was developed. Further hydrolysis of the methyl esters was achieved using LiOH to give the final products 7a-7d.[7] Table 2a Synthesis of targeted vancomycin derivatives.
Table 1a Synthesis of various methyl 2-aloxy-3-oxopropanoates.
2
Entriy 1
2
3
4
5
6
7
Substrates 1a
1a
Reaction conditions NaBH(OAc)3/ DMF
Products O O O NH 6a Vancomycin
NaBH(OAc)3/ THF
6a
1a
NaBH3CN/ DMF
1a
NaBH3CN/ DMF/AcOH
1b
1c
1d
NaBH3CN/ DMF/AcOH
Yield[%]
0
0
62
6a
54
O NH Vancomycin
2
8
2
chlorobiphenyl vancomycin
S0960-894X(14)00329-1 http://dx.doi.org/10.1016/j.bmcl.2014.03.093 BMCL 21486
To appear in:
Bioorganic & Medicinal Chemistry Letters
Received Date: Revised Date: Accepted Date:
4 December 2013 23 March 2014 25 March 2014
Please cite this article as: Gu, W., Chen, B., Ge, M., Design and Synthesis of New Vancomycin Derivatives, Bioorganic & Medicinal Chemistry Letters (2014), doi: http://dx.doi.org/10.1016/j.bmcl.2014.03.093
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Design and Synthesis of New Vancomycin Derivatives Wen Gua, Bei Chena, Min Gea,b,* a
College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 210009, China b.
Acesys PharmaTech, Inc., Science and Technology Building 24B, 5 Xing Mo Fang Road, Nanjing, 210009, China
This is where the receipt/accepted dates will go; Received Month XX, 2000; Accepted Month XX, 2000 [BMCL RECEIPT]
Abstract—A set of vancomycin derivatives with lipid chain attached via a glyceric acid linker was designed and synthesized. A concise synthesis towards these derivatives was developed and the IC50s of these new lipoglycopeptides were tested. Some of them showed very potent activity against both vancomycin sensitive and resistant strains.
The glycopeptides antibiotics are the most important drugs in current use for the treatment of Gram-positive bacterial infections. They function through binding to the bacterial cell wall substrate DAla-D-Ala and thus inhibiting the transpeptidation step. In 1990s, vancomycin resistant enterococci (VREs) and vancomycin-resistant staphylococcus aureus (VRSA) emerged which posed a very serious public health problem. This led to new interests in the development of antibiotics of different class as well as new derivatives of the glycopeptides.
HO R 1 NH OH O OH Me O
Me
OH O O O R2 O O O
N H H
HN HO
O
H N O
HO
------------------------------* Corresponding author. Tel.: +86 025 83421757; fax: +86 025 83172563; e-mail: [email protected]
N H O
OH O
H N O
N H
H N Me
OH OH
vancomycin: Oritavancin:
Many different types of vancomycin derivatives were prepared and studied. The most successful finding is the discovery by Nagarajan et al that attaching lipid chain to the vancomycin carbohydrate portion led to significant potency boost towards both vancomycin sensitive and resistant strains.[1] These modifications eventually led to the development of a new glycopeptide antibiotic called oritavancin which is now close to FDA filing (Figure 1). Studies suggest that these new vancomycin derivatives with lipid chain attached (lipoglycopeptides) have dual mechanisms by inhibiting both transpeptidation and the transglycosylation steps of the cell wall biosynthesis.[2] The alycone portion binds the cell wall substrate and the lipid carbohydrate portion inhibits the transglycosylases at the same time. Interestingly, we notice that another transglycosylase inhibitor – moenomycin (Figure 1) also has a similar structure feature where a long lipid chain is attached to its carbohydrate portion via a glyceric acid linker. Kahne group has extensively studied the functions of the C55 lipid chain as well as the carbohydrate portion.[3] However, the function of this glyceric acid phosphate linker remains unknown.
Cl
NH2
C O
O
Cl
O HO HO O OH HO NH H3C O O HO OH HO
R1=H, R2=H R1=
Cl
H 2N HO
OH O
O
O
O CH 2 O OH O O HO NHAc NHAc O O
P
HO Me
NH 2 O Me O
CH 3 O NH 2 O
O
O
R2=
O OH
HO2C
Moenomycin Figure 1. Chemical structures of vancomycin, oritavancin and moenomycin.
During the development of the lipoglycopeptides, it was found that these derivatives have poorer solubility in water compared to vancomycin. In addition, the greasy chain caused unwanted ion-channel side effect. How to improve aqueous solubility while improving the potency is a challenging problem in this area. We have noticed the similarity between the lipoglycopeptides and moenomycin. It was interesting to understand the role of the glyceric acid-phosphate portion of moenomycin is. Here we designed a set of vancomycin derivatives with lipid chains attached to the carbohydrate portion via a similar glyceric acid linker. Our assumption is that an important structural feature “borrowed” from a transglycosylase inhibitor should
1
also be helpful to the transglycosylase inhibiting effect of the vancomycin carbohydrate portion. In addition, the added polarity of this acid linker should also help to lower the LogP, improve the solubility and reduce the unwanted ion channel side effect. On the other hand, studies on these analogs may also give us some hints of the role of this glyceric acid linker in moenomycin. A straightforward way for making these new derivatives is through the reductive-amination between ester 1 and vancomycin (Scheme 1). We tried a few methods to make this unique ester. At first, we converted serine into methyl 2-bromo-3hydroxypropanoate 2 through diazonium reaction and esterification. However, all attempts to displace the alfa-bromide with alkoxide only led to the decomposition of 2. We then tried the Kahne procedure and prepared the ester 5.[4] However, the final oxidation of the hydroxyl group failed completely with every oxidation reagent we tried, presumably due to the instability of the final product. Scheme 1a. Attempted syntheses of compound 1. OH O
a, b
O OMe
OMe
OH Br
NH2
OH OH OH
O
OH O
c, d, e
OR
2
OH OH OR
f, g
1
OH O OMe
OH OH OH 3
OR OH OH 4
OR 5
a
Reagents and conditions: (a) NaNO2, HBr; (b) MeOH, HCl; (c) PMB dimethoxy ketal, TsOH; (d) RBr, NaH; (e) AcOH, H2O; (f) NaIO4, THF, H2O; (g) NaClO2, NaH2PO4, H2O, 2-methyl-2-butene; then MeOH, HCl.
After lots of literature searching and experimentation, we found that the condensation of methyl 2-benzoxy-acetate with methyl formate can provided the sodium salt of desire product in one single step (entry 1, table 1).[5] The product is quite stable as potassium salt. This method can also be applied to other 2-alkoxy-acetates to give a series of 3-oxy propionates. Proton NMR indicated that these compounds are in their enolate form which makes them much more stable.
a,b R-OH
O RO
Entry
R=
1
benzyl
c
O-K+ O OMe
OMe
OR
Product
Yield[%]
OMe O
63
O 1a
+ -
KO
OMe 2
chlorobiphenyl methyl
O
Cl O
+ -
KO O
3
n-butyl
OMe 66
+K - O
O 1c O
4
n-hexyl
79
1b
OMe 55
+K- O
1d
O
a
Reagents and conditions: (a) chloroacetic acid, NaH, THF; (b) SOCl2, MeOH; (c) KOtBu, methyl formate, ether.
Next we studied the reductive-amination reaction between compounds 1a-1d and vancomycin. Following the known condition (DMF, NaBH3CN, 80℃)[1], we only obtained the enamine intermediate. Attempts to reduce this intermediate with various reducing agents all failed (entry 1, 2, 3, table 2). During the isolation of this intermediate, we noticed that it was less stable under acidic conditions. With this in mind, we adjusted the acidity of the reaction media. A 1:1 mixture of DMF and acetic acid turned out to be the best reaction solvent and high temperature (80 ℃) was also needed. Complete reduction of the enamine intermediate was achieved to give 6a (entry 4, table 2) [6]. Compounds 6b-6d were synthesized in similar fashion (entry 5-8, table 2). Thus, a concise synthesis of these vancomycin derivatives with lipid-glyceric linker was developed. Further hydrolysis of the methyl esters was achieved using LiOH to give the final products 7a-7d.[7] Table 2a Synthesis of targeted vancomycin derivatives.
Table 1a Synthesis of various methyl 2-aloxy-3-oxopropanoates.
2
Entriy 1
2
3
4
5
6
7
Substrates 1a
1a
Reaction conditions NaBH(OAc)3/ DMF
Products O O O NH 6a Vancomycin
NaBH(OAc)3/ THF
6a
1a
NaBH3CN/ DMF
1a
NaBH3CN/ DMF/AcOH
1b
1c
1d
NaBH3CN/ DMF/AcOH
Yield[%]
0
0
62
6a
54
O NH Vancomycin
2
8
2
chlorobiphenyl vancomycin
