Regioselective glycosylation of novobiocin alters activity

Article abstract of DOI:10.1016/j.carres.2017.10.011

Glycosylation is a promising approach to overcome antimicrobial drug resistance. In this study, we investigated Koenigs-Knorr and phase transfer glycosylation on novobiocin. While the former only gave a 4′-OH product, the later produced mainly a kinetic c

Full text of DOI:10.1016/j.carres.2017.10.011

Accepted Manuscript
Regioselective glycosylation of novobiocin alters activity
Guoxuan Sun, Pedro Ernesto de Resende, Paul Stapleton, Martyna Kuta, Xiangtao
Wang, Shozeb Haider, Min Yang
PII:
S0008-6215(17)30687-0
10.1016/j.carres.2017.10.011
CAR 7465
DOI:
Reference:
To appear in: Carbohydrate Research
Received Date: 14 September 2017
Revised Date: 13 October 2017
Accepted Date: 18 October 2017
Please cite this article as: G. Sun, P.E. de Resende, P. Stapleton, M. Kuta, X. Wang, S. Haider, M.
Yang, Regioselective glycosylation of novobiocin alters activity, Carbohydrate Research (2017), doi:
10.1016/j.carres.2017.10.011.
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ACCEPTED MANUSCRIPT
Graphical abstract
Regioselective glycosylation of novobiocin can be achieved via different reaction conditions which lead to variation of
activity.

ACCEPTED MANUSCRIPT
Regioselective Glycosylation of Novobiocin Alters Activity
Guoxuan Sun,a Pedro Ernesto de Resende,a Paul Stapleton,a Martyna Kuta,a Xiangtao
Wang,b Shozeb Haider,a and Min Yang a*
a. The School of Pharmacy, University College London, 29/39 Brunswick Square, London,
WC1N 1AX, UK
b. The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &
Peking Union Medical College, Beijing, 100193, China
Corresponding author: min.yang@ucl.ac.uk
Abstract: Glycosylation is a promising approach to overcome antimicrobial drug resistance. In this
study, we investigated Koenigs-Knorr and phase transfer glycosylation on novobiocin. While the
former only gave a 4'-OH product, the later produced mainly a kinetic controlled 5-OH product, but
still achieved the 4'-OH modification and novoise-glycosylated products (with stronger base), as well
as a diglycosylated compound. Investigation on the antibacterial activity indicate that the presence
of galactose moiety helps to improve activity possibly via enhanced cellular uptake.
1. Introduction
Antimicrobial agents are the last line of defence against microorganisms. Overuse and/or misuse of
antibiotics has been linked to resistant organisms such as multidrug resistant (MDR) Gram-negative
bacteria, methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci
(VRE). Such organisms are responsible for 25,000 deaths each year and more than €1.5 billion in
healthcare-associated expenses and productivity losses in Europe alone.[1] Consequently, efforts
have now hastened to find new strategies to address the increasing resistance problem; one
promising approach is to modify a compound by glycosylation.[2] Many antibiotics are glycosylated
and contain a variety of different sugars.[3-7] Glycosylation modifies antimicrobial agent
pharmacokinetic parameters such as solubility, membrane transport, pharmacodynamics,
mechanism and potency.[8] The sugar residues can increase or decrease potency[9, 10] either by
being directly involved in the binding process [11, 12] or by being essential for antimicrobial activity
[13].
Novobiocin is a member of the aminocoumarin family and acts as a bacterial DNA synthesis inhibitor
by binding to the B subunit of the DNA gyrase.[14] It also possess anticancer activity by binding to
the HSP90 chaperone.[15, 16] The clinical use of this class of antibiotics has been restricted due to
their low water solubility, low activity against Gram-negative bacteria [17] and toxicity in vivo.[18]
Modifications of aminocoumarins have been made to achieve better activity in the past decade.[19-
22] Previously we discovered that novobiocin can be glycosylated by glycosyltransferases. This

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simple glycosylation separates the anticancer activity from antibacterial activity up to 2.67×104
fold.[23] However, the exact mechanism is not fully clear.
2. Result and discussion
2.1 Phase transfer glycosylation
Previously, the glycosylated novobiocins were obtained either via enzymatic catalyzed synthesis,
which was difficult to scale up or involves the use of mercury cyanide which is extremely toxic. In
order to find an alternative synthetic route, we tested a few conditions, such as Koenigs-Knorr (Fig.
1, Table 1) and phase transfer glycosylation ( Fig. 2, Table 2) with different solvents, catalysts and
temperature. In the Koenigs-Knorr reactions, only DMF, a polar aprotic solvent, gave reasonable
yield (31%) with the tetra-acetylated glucosyl bromide donor and novobiocin due to its strong
solvent effect and capacity to fully solubilise novobiocin. Adding catalyst or increase temperature led
to a decrease the yield (Table 1) probably because the reaction was slow and a fast forming oxinium
intermediate was not in favour of the desired product. However, it should be noted that under these
conditions, only glycosylation on the 4'-OH was formed (Fig. 1, Fig. S1).
R2
R2
R1
O
5
OH
R1
O
OH
HO
HO
H
AcO
AcO
OH
OAc
N
4'
O
Catalyst
Solvent
Equivalent
Temperature
O
OH
O
O
OH
O
O
H
CH3
H
O
N
NaOMe
MeOH
H3CO
N
2"
4'
O
4'
O
O
OH
O
O
Novobiocin (1)
O
O
O
O
O
+
H2N
CH3
CH3
O
O
H3CO
R1
H3CO
OAc
O
2
3
R1 = OAc, R2 = H,
R1 = H, R2 = OAc,
O
O
OH
R1 = OAc, R2 = H, 4
R1 = H, R2 = OAc,
R2
OH
O
AcO
AcO
O
5
H2N
H2N
Br
Figure 1. Glycosylation with Koenigs-Knorr condition.
Table 1.Glycosylation of novobiocin with various conditions.
No
1
Solvent
THF
Catalyst
Hg(CN)2
AgBF4
AgOTf
CuOTf
no
Eqv.
1.2
1.1
1.1
1.1
1.1
1.1
1.1
1.2
1.1
1.1
1.1
1.1
RT /min
Mass (ESI +)
Yield
57%
-
Temp/°C
rt
rt
rt
rt
rt
45
rt
rt
rt
rt
rt
rt
3.78
-
943
-
2
THF
3
THF
3.82
-
-
Trace
-
4
THF
-
5
DMF
DMF
DMF
DMF
DMF
DMF
DMF
PC
3.82
3.81
3.82
3.81
3.81
3.80
-
943
943
943
943
943
943
31%
14%
17%
11%
10%
9%
6
no
7
AgCO3
BiONO3
AgOTf
K2CO3
LiBr
8
9
10
11
12
no
3.79
943
15%

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Eqv: Equivalent. rt: room temperature. RT: retention time. Yield: estimated from LC UV spectra. PC:
Propylene carbonate.
Phase transfer reaction conditions (Fig. 2, Table 2) suggested that chloroform was a better solvent
than DCM and that a higher equivalent of benezyl tributyl ammonium bromide (BTAB) and stronger
2-
-
(CO3 vs HCO3 ) base favoured a better yield. However, it should be stressed that it produced a
different glycosylation product with different retention time (4.6 min instead of 3.8 min, Table 2, Fig.
S2). Ion trap analysis; while all major MS3 peaks could be confidently assigned, the ion of 518.08
proved a 5-OH glycosylation (Fig. 2). The structure was further validated by NMR (Table S1) - a
coupling between H1''' and C5 indicated the linkage. At elevated temperature (Table 2, No 19) the
4'-OH (3.8 min) and 5-OH glycosylated products could be observed as well as a diglycosylated
product (Fig. S3). As the 5-OH is more accessible but with higher pKa values [23] compared to 4'-OH,
this probably means that the increase in temperature changed the reaction from kinetic to
thermodynamic control. The much stronger base (OH-) caused decarbamation of novobiocin and its
glycosylated product, but produced another glycosylated product (4.98 min) which may possibly
occur on the 2''-OH in noviose (Table. 2, No 20, Fig. S4).

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Figure 2. Glycosylation with phase transfer condition and MS/MS analysis of products. Top: reaction
scheme; bottom: MS/MS analysis of compound 6 to elucidate the structure. MS1: full MS spectrum.
941.34, [M-H+]-. MS2: MS/MS analysis of 941. Peaks of 898.36 and 724.32 are indicated in the
reaction scheme (red cleavage). MS3: MS3 analysis of 724.32 in MS2. The peak of 518.08 indicated
that glucose moiety was added onto the phenol-OH (5-OH). Peaks of 682.32 and 664.22 are
indicated in the scheme (Top, green cleavage). Peak of 621.97 was formed from peak 664.22 by
removing one of the acetyl groups
Table 2. Phase transfer condition for the synthesis of glucosyl-novobiocin.
Entry Promoter
Eqv.
Water/Organic
Donor
/Eqv.
1.1
RT/min
Mass
(ESI+)
Yield
Temp/°C
13
14
15
16
17
18
19
BTAB
BTAB
BTAB
BTAB
BTAB
BTAB
BTAB
0.1
0.1
0.1
1
Water/DCM
rt
rt
-
0.1M NaHCO3/DCM
0.15M K2CO3/ DCM
0.15M K2CO3/DCM
0.15M K2CO3/DCM
0.15M K2CO3/CHCl3
0.15M K2CO3/CHCl3
1.1
1.1
1.1
4
-
rt
4.59
4.60
4.59
4.60
3.76
4.10
943
943
943
943
943
1273
12%
16%
30%
45%
28%
29%
rt
1
rt
1
4
rt
1
4
45
4.55
4.42
4.68
943
570
900
9%
20
BTAB
1
0.08 M KOH/CHCl3
4
rt
25%
25%
4.98
943
18%
Note: BTAB: Benzyltributylammonium Bromide. rt, room temperature. RT: retention time. 4-
glycosylated product marked in red. Phenol-glycosylated product marked in blue. There is also an
unidentified product marked in green which could be another glycoside of novobiocin due to its
identical molecular weight. Yield: estimated from LC UV spectra.
In No 19, product RT=4.10 min is characterized as double-glycosylated product of novobiocin.
In No 20, product RT=4.42 min is characterized as novobiocin lost its carbamate group located on
novoise sugar. As a result, product RT=4.68 min is the glycoside of product RT=4.42 min.
Figure 3 shows the HMBC-NMR of compounds 4 & 5, obtained in the presence of DMF alone. Both
H1''' from a sugar coupled with C4' in the coumarin ring clearly proved the glycosylation on the 4'-
OH position. While most other peaks retain the same chemical shifts both in HNMR and CNMR, the
sugar moiety (red for glucose and blue for galactose) showed quite different shift and coupling
constants, especially H4'''. Most three bonds long range couplings could be observed such as within
the 2 ppm and 65 ppm regions, and a proton from an acetyl group coupled to 2''' to 6''' respectively,
but not 5'''. Compounds 2 & 3 were obtained by deprotection of 4 &5 respectively according to
procedures reported previously. [23]

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*
Figure 3. Combined HMBC NMR analysis of tetra-O-acetyl-β-glucosyl-novobiocin (Red) and
galactosylnovobiocin (Blue). Both spectra indicated the binding between H1''' to 4' (Green). Long
1
range couplings can be observed on acetyl CH3 to 2''' to 6''' but not 5'''. Unlabelled peaks are H
coupled 13CNMR peak. *: solvent residues.
2.2 Biological activity test
Novobiocin inhibits DNA supercoiling catalyzed by DNA gyrase. DNA gyrase activity assays were
carried out on 1, 2 and 3 (Fig. 4). 1 showed inhibition at 0.5 µM, which is consistent with the value
reported in the literature (0.9 µM[24]). 2 and 3 inhibited DNA gyrase at 5 and 10 µM, respectively.
This indicates that adding a sugar residue on novobiocin reduced the DNA gyrase-binding capacity of
the compound.
The crystal structure of the DNA gyrase (PDB id:1AJ6) was used as a receptor in docking studies using
ICM-Pro Molsoft software.[25] Compound 1 was re-docked to the same position within the crystal
structure, the binding energy of1 (-25.84 kcal/mol), 2 (-21.32 kcal/mol) and 3 (-19.35 kcal/mol) are in
agreementwith the gyrase assay result. Compounds 2 and 3 are in the same position as compound 1,
with noviose moieties in the pocket. In all three cases, we observed hydrogen bond between ligands

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(noviose moieties) and residues N46, T165 and D73, which contribute to the binding pocket. The
added sugar in 2 and 3 creates new hydrogen bonds with residue R76 (Fig. 4).
The in vitro antibacterial activities of 1- 5 were evaluated against several clinically relevant bacteria
(Table S2). Neither novobiocin or modified novobiocin derivatives showed strong antibacterial
activity against various strains. Galactosyl-novobiocin (3) showed about 2-fold increased potency
probably due to the enhanced uptake via permease exploiting the galactose residues, which was
reported previously.[26]
Figure 4. Antibiotics effect of compounds 1-3. a) Effect on the capacity of DNA gyrase to supercoiled
relaxed pBR322 DNA.-, relaxed pBR322 without DNA gyrase; OC, open circular plasmid DNA; C,
coiled plasmid DNA; SC, supercoiled, unit: µM. Top: Novobiocin (1); Middle: glucosyl_novobiocin (2)
and Bottom; galactosyl_novobiocin (3).[23] b) DNA gyrase protein structure (PDB ID: 1AJ6) with re-
docked 1 (violet), and docked compound 2 (pink) and 3 (blue). Both2 &3 interact with the pocket in
the same way like 1 by creating four hydrogen bonds between the noviose moiety and residues N46,
T165 and D73. The glucose/galactose moieties create new hydrogen bonds with residue R76. Yellow
lines: hydrogen bonds. c) A zoomed-out image of glucose/galactose binding positions from b).
3. Experimental
3.1 General method of Koenigs-Knorr glycosylation (Table1, 1-4)
A mixture of novobiocin sodium (2.0g, 3.159mmol), 1-Bromine-2,3,4,6-tetra-O-acetyl-α-D-
glucose/galactose (1.32g, 3.218 mmol), activated4Å molecular sieves (approx. 6 g) and anhydrous
THF (100mL) were added into a 250ml flask. Catalyst (1.0eqv) was added into the system and then
the reaction mixture was stirred for 7 days under nitrogen at room temperature covered by foil and
monitored by LC/MS (Shimazu 2020, Column: XTerra, C-18, 2.5um,4.6mm, solvent A 0.1 FA in water,
solvent B 0.1%FA in ACN, t = 0, 10% B, t = 4 min, 95% B, t = 5.2 min, 10% B, t = 7 min, 10% B. The
reaction mixture was filtered and washed with potassium iodide (2M, 25mL×2 if used Hg(CN)2),
saturated NaHCO3 (10 mL×2) and dried with sodium sulphate.The solvent was removed by vacuum

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to afford a light brown crude product. Then the crude product was purified by flash column (ethyl
acetate/petroleum ether/methanol 12/4/1,) to afford a white powder (yield; see Table 1)
3.2 Generalmethod of glycosylation using DMF as solvent (Table 1, 5-12)
A mixture of novobiocin sodium (200 mg, 0.32 mmol), 1-Bromine-2,3,4,6-tetra-O-acetyl-α-D-
glucose/galactose (0.132g, 0.32mmol), activated 4Å molecular sieves (approx. 1.5g) and anhydrous
DMF (anhydrous, 20ml, or other solvent as in Table 1) were added into a 250 ml flask. Catalyst (eqv.
shown in Table 1) was added into the reaction. The reaction mixture was stirred for 3 days under
nitrogen gas protection at room temperature covered by foil and monitored by LC/MS. Water
(120ml) was added into the system and the crude product was extracted by chloroform. The crude
product was purified by flash column (ethyl acetate/petroleum ether/methanol 12/4/1, Rf = 0.3) to
afford a white powder (yield; see Table 1).
3.3 General method of phase transfer glycosylation of novobiocin
Novobiocin (20mg 0.03mmol) was weighed and dissolved in a beaker that already contained 5 ml
0.15 M potassium carbonate water solution, stirred for 15 minutes. α-1-Bromine-2,3,4,6-tetra-O-
acetyl-D-glucose (53.9mg, 0.12mmol) and benzyltributylammonium bromide (11.4mg, 0.03mmol)
were dissolved in 5ml chloroform. When the stirring of water-phase was complete, the colourless
solution inside the beaker was transferred into the flask and little amount of 0.15M potassium
carbonate water solution was used to wash the beaker. Once the separation of two layers was
finished, the whole system was put into a 45°Coil bath (or room temperature) and stirred overnight.
Organic layer was monitored by LC/MS. The water phase inside was removed and the organic phase
was washed with saturated NaHCO3 (20mL), brine (10mL) and deionized water (10mL× 2). The brown
organic phase was then concentrated under vacuum to obtain an orange solid residue and purified
by Biotage reverse phase column (yield see Table2). Compound 6 was separated using prep-HPLC
under linear gradient condition within 200 min. 1HNMR (400 MHz, MeOD4): δ = 7.66 (1 H, s, H3), 6.01
(1 H, d, J = 8.8 Hz, H6), 7.67 (1 H, d, J = 8.9 Hz, H7), 3.12 (2 H, m, H8), 5.10 (1 H, m, H9), 1.54 (6H, s,
H11, H12), 7.63 (1 H, d, J = 8.8 Hz, H5'), 7.00 (1 H, d, J = 8.7 Hz, H6'), 2.11 (3 H, s, H11'), 5.36 (1 H, d, J
= 1.88 Hz, H1''), 4.04 (1 H, m, H2''), 5.15 (1 H, dd, J = 3.18, 9.93 Hz, H3''), 3.40 (1 H, d, J = 12.6 Hz,
H4''), 1.16 (3 H, s, H6''), 0.98 (3 H, s, H7''), 3.37 (3 H, s, H8''); 5.20 (1 H, d, J = 7.9 Hz, H1'''), 5.26 (1 H,
m, H2''''), 5.30 (1 H, m,H3''''), 5.12 (1 H, m, H4''''), 4.18 (1 H, m, H5''''), 4.03 (2 H, m, 2 * H6''''), 1.80-
2.01 (12 H, s, 4*CH3CO).13CNMR (125 MHz, MeOD4): δ = 169.35 (C1), 158.35 (C2), 130.77 (C3), 125.03
(C4), 159.15 (C5), 110.41 (C6), 128.23 (C7), 29.16 (C8), 123.21 (C9), 134.0 (C10), 26.11(C11), 18.06
(C12), 163.16 (C2'), 108.84 (C3'), 164.52 (C4'), 124.00 (C5'), 115.09 (C6'), 158.15 (C7'), 114.46 (C8'),
153.33 (C9'), 118.18 (C10'), 6.56 (C11'), 99.91 (C1''), 71.07 (C2''), 73.20 (C3''), 82.85 (C4''), 79.83 (C5''),

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29.08 (C6''), 23.34 (C7''), 61.87 (C8''), 167.30 (C9''), 99.84 (C1'''), 70.21 (C2'''), 68.85 (C3'''), 72.34
(C4'''), 72.34 (C5'''), 62.73 (C6'''),20.58-20.83 (4*CH3CO), 171.25-172.09 (4*CH3CO). ESI+811 [M+H]+,
HRMS: 943.3360, calculated for C45H54N2O20: 943.3348.
3.4 DNA Gyrase Assay
The DNA gyrase assay was performed according to the supplier’s procedure withnovobiocin,
glucosyl-novobiocin and galactosyl-novobiocin as inhibitors.
DNA gyrase (1U) wasincubated with relaxed pBR322 (0.5μg) in a reaction volume of 30 μL at 37°C for
1 hr in TRIS-HCl (35mM, pH 7.5), KCl (24mM), MgCl2 (4mM), DTT (2mM), spermidine (1.8mM), ATP
(1mM), glycerol (6.5%, w/v) and albumin (0.1mg/mL).
After incubation the mixture was treated with equal volumes of chloroform /isoamyl alcohol (24:1)
and the end point was determined by separating relaxed and super twisted plasmid pBR322 DNA by
agarose gel electrophoresis (0.8% agarose with TBE buffer), running without ethidium bromide.
After electrophoresisthe gel was soaked in tank buffer containing ethidium bromide for one and half
hours.
3.5 Docking studies and visualization
The crystal structure of the DNA gyrase (PDB id:1AJ6) was used as a receptor in docking studies. The
ICM-Pro Molsoft software (Molsoft LLC, www.molsoft.com) was used to carry out the docking
studies. Ligand No. 1 (novobiocin) was extracted from crystal structure and redocked in the same
position. The parameters used in obtaining the redocked conformation were used to dock other
ligands. ICM lig-edit module was used to generate ligand 2 and. 3. A binding pocket was defined by
using ICM Finding Pocket tools. The docking grid was centred on the best pocket found, taking into
account all residues around existing ligand (novobiocin). For each compound we used the APF
superposition template method to obtain the most reliable results. The hydrogen bond analysis of
obtained complexes was carried out with ICM Molsoft software.
3.6 Activity of novobiocin and novobiocin derivatives against Escherichia coli
The MICs of novobiocin and novobiocin derivatives were determined by micro-broth dilution
technique in cation-adjusted Mueller-Hinton broth and with a bacterial inoculum of 5x105 CFU/ml.
Microtitre plates were incubated aerobically at 37ºC and read after 24h. The concentration range
tested was 128 to 0.12µg/ml.
4. Conclusions
In conclusion, Koenigs-Knorr glycosylation gave only a thermodynamic controlled 4'-OH product.

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DMF proved to be the best condition, while other conventional catalysts were detrimental to the
yield. Phase transfer reaction gave a kinetic controlled 5-OH product but still produced
thermodynamic controlled 4'-OH, di-glycosylated glycosylation products and, possibly the more
difficult 3''-OH glycosylation in the presence of a stronger base. This provides a powerful tool to
generate various products. It also demonstrated that the galactose modification increased the
antimicrobial activity probably due to the enhanced uptake ability.
Highlights
•
•
•
•
Reaction conditions control glycosylation position.
Glycosyl-novobiocin weaken the binding to DNA gyrase.
Sugar moiety created new additional binding to the protein target.
Galactosylation may enhance the activity against certain E. coli isolates.
Keywords
Glycosylation; Novobiocin; Phase transfer reaction; Antibacterial activity.
Acknowledgement
This work was supported by EPSRC (EP/K023071/1). We thank Dr Andreia M. R. Guimaraes for her
technical help.
Declaration
The authors declare no conflict of interest.
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