Báo cáo khoa học: Thiamin diphosphate in biological chemistry: analogues of thiamin diphosphate in studies of enzymes and riboswitches pot

MINIREVIEW
Thiamin diphosphate in biological chemistry: analogues
of thiamin diphosphate in studies of enzymes
and riboswitches
Kwasi Agyei-Owusu and Finian J. Leeper
Department of Chemistry, University of Cambridge, UK
Thiamin diphosphate 1 (ThDP) (Fig. 1) is a coenzyme
that assists in the catalysis of carbon–carbon bond-
forming and bond-breaking reactions adjacent to a
carbonyl group. A large and diverse collection of
enzymes require ThDP, which acts as an electron sink
during catalysis, stabilizing what would otherwise be
an acyl carbanion in the form of an enamine interme-
diate (Fig. 2). These enzymes include pyruvate decar-
boxylase (PDC; EC 4.1.1.1) which is involved in the
formation of alcohol in anaerobic fermentation [1],
transketolase (TK; EC 2.2.1.1) which transfers a two-
carbon unit from a ketose to an aldose [2] and
pyruvate dehydrogenase (PDH; EC 1.2.4.1), a highly
complex enzyme that links the glycolytic pathway to
the citric acid cycle through the formation of acetyl
CoA [3].
The general catalytic cycle for ThDP-dependent
enzymes, as illustrated by the cycle for PDC (Fig. 2),
was first elucidated by Breslow [4] and begins with
deprotonation of the C-2 carbon of the thiazolium ring
(now believed to be effected by the 4¢-N atom of the
aminopyrimidine ring in its imino tautomer). The
resulting ylid subsequently carries out a nucleophilic
attack on the keto group of pyruvate, followed by
decarboxylation which leads to formation of the enam-

ine intermediate (which can also be drawn as an
Keywords
acetohydroxyacid synthase; enzyme crystal
structure; enzyme inhibition; pyruvate
decarboxylase; pyruvate dehydrogenase;
reaction mechanism; riboswitch; thiamin
pyrophosphate; thiamine diphosphate;
transketolase
Correspondence
F. J. Leeper, Department of Chemistry,
University of Cambridge, Lensfield Road,
Cambridge CB2 1EW, UK
Fax: +44 1223 336362
Tel: +44 1223 336403
E-mail:
Website: />fjl.html
(Received 9 October 2008, revised 9 March
2009, accepted 12 March 2009)
doi:10.1111/j.1742-4658.2009.07018.x
The role of thiamin diphosphate (ThDP) as a cofactor for enzymes has
been known for many decades. This minireview covers the progress made
in understanding the catalytic mechanism of ThDP-dependent enzymes
through the use of ThDP analogues. Many such analogues have been syn-
thesized and have provided information on the functional groups necessary
for the binding and catalytic activity of the cofactor. Through these studies,
the important role of hydrophobic interactions in stabilizing reaction inter-
mediates in the catalytic cycle has been recognized. Stable analogues of
intermediates in the ThDP-catalysed reaction mechanism have also been
synthesized and crystallographic studies using these analogues have allowed
enzyme structures to be solved that represent snapshots of the reaction in

progress. As well as providing mechanistic information about ThDP-depen-
dent enzymes, many analogues are potent inhibitors of these enzymes. The
potential of these compounds as therapeutic targets and as important her-
bicidal agents is discussed. More recently, the way that ThDP regulates the
genes for its own biosynthesis through the action of riboswitches has been
discovered. This opens a new branch of thiamin research with the potential
to provide new therapeutic targets in the fight against infection.
Abbreviations
3-deazaThDP, 3-deazathiamin diphosphate; PDB, Protein Database; PDC, pyruvate decarboxylase; PDH, pyruvate dehydrogenase; PDHc,
pyruvate dehydrogenase complex; ThDP, thiamin diphosphate; ThTDP, thiamin 2-thiazolone diphosphate; ThTTDP, thiamin 2-thiothiazolone
diphosphate; TK, transketolase; TPK, thiamin pyrophosphokinase.
FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS 2905
a-carbanion resonance structure). Depending on the
ThDP-dependent enzyme involved, the enamine can
attack a number of electrophilic species. In the case of
PDC, protonation of the enamine occurs and finally
release of acetaldehyde regenerates the ThDP ylid.
Over the course of the last 70 years, numerous ana-
logues of ThDP have been synthesized by various
research groups and this has afforded us an insight
into the catalytic mechanism of ThDP-dependent
enzymes [4]. Binding and inhibition studies, as well as
X-ray crystallography involving ThDP analogues, have
provided us with information on enzyme ⁄ coen-
zyme ⁄ substrate interactions and how reaction interme-
diates are stabilized by the enzyme. More recently,
work on various enzymes as targets for antitumour
and antimalarial drugs based on ThDP has been pur-
sued with some promise [5,6]. With the discovery of
ThDP-reponsive riboswitches [7], an exciting field for

exploration has recently been opened up: the regula-
tion of thiamin biosynthesis in some organisms by
ThDP riboswitches offers a novel target for drugs
based on thiamin. This minireview covers the key
enzymatic studies of ThDP analogues that have aided
our mechanistic understanding of ThDP-dependent
enzymes, as well as studies of thiamin analogues as
drug molecules and in the field of riboswitches.
Modifications to the aminopyrimidine
moiety
Analogues of ThDP with a modified aminopyrimidine
moiety (Fig. 3) provided a key insight into binding of
the coenzyme as well as its catalytic activity. Schellen-
berger et al. synthesized a number of pyridyl and dea-
minopyrimidine species for testing on the apoenzymes
of PDC, PDH and TK [8,9]. The N
1
0
-pyridyl analogue
(in which the 3¢-nitrogen has been replaced by carbon)
was found not only to bind to the apoenzymes tested,
but also to be catalytically active. It was concluded
that the 3¢-nitrogen was not crucial for binding or cat-
alytic activity. The N
3
0
-pyridyl analogue (in which the
1¢-nitrogen has been replaced by carbon), however,
was found to bind relatively weakly and produce no
discernible catalytic activity. From this result, it could

Fig. 2. Catalytic mechanism for pyruvate
decarboxylase.
Fig. 1. Thiamin diphosphate.
Studies with analogues of thiamin diphosphate K. Agyei-Owusu and F. J. Leeper
2906 FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS
be concluded that hydrogen bonding between a suit-
able amino acid residue and the N
1
0
nitrogen was not
only required for tight binding, but also was critical
for the catalytic activity of the coenzyme. It was subse-
quently discovered by X-ray crystallography, site-spe-
cific mutagenesis and NMR studies of coenzyme
analogues that there is a conserved glutamate residue
in the active site of thiamin-dependent enzymes that
hydrogen bonds to the N
1
0
nitrogen (Fig. 4) [10] and
the consequence of this hydrogen bonding is to
increase the basicity of the 4¢-amino group, its ability
to act as a proton acceptor for the C2–H of the thiazo-
lium ring being enhanced by several orders of magni-
tude [11].
By deleting the 4¢-amino group altogether or replac-
ing it with other functionalities such as a thiol,
hydroxy or dimethylamino group, its important role in
catalysis soon became apparent [9]. These analogues
generally showed good binding capacity but were cata-

lytically inactive, offering further proof of the proton
acceptor role of the amino group. One exception is the
4¢-monomethylated amino group which has been
shown to retain catalytic activity when bound to trans-
ketolase with b-hydroxypyruvate as substrate [12].
However, the stability of the resulting enamine inter-
mediate was reduced significantly. It was suggested
that this is caused by impaired hydrogen bonding
between the amino group and the dihydroxyethyl
group attached to C-2.
It has been shown that ThDP adopts a specific con-
formation in the active site of the enzyme [13]. This
so-called ‘V-conformation’ was first suggested when
6¢-methylated ThDP analogues were tested for enzymic
activity by Schellenberger [9]. For PDC, it was
reported that 6¢-methyl-ThDP was catalytically inac-
tive, whereas 4-demethyl-6¢-methyl-ThDP was active.
It was proposed that a 6¢-methyl group causes a steric
clash with the 4-methyl group when the ThDP is in
the V-conformation and the analogue therefore has to
adopt an altered conformation. Interestingly, the
4-demethylated analogue, which retains its catalytic
activity, is a relatively weak binder to the apoenzyme,
suggesting the requirement of hydrophobic interactions
between the 4-methyl group and the apoenzyme for
good binding affinity. It was later reported that in
transketolase the 6¢-methyl-ThDP does have $ 50% of
the normal catalytic activity [14], whereas the 4-dem-
ethyl-6¢-methyl-ThDP is inactive [15].
Crystal structures of three of these pyrimidine-modi-

fied analogues, 1¢-pyridyl-, 3¢-pyridyl- and 6¢-methyl-
ThDP, bound to transketolase have been obtained
[16]. The pyrimidine ring is found in a very similar
position to that of the normal ThDP complex in
all three analogues, confirming that the lack of
activity of the N
3
0
-pyridyl analogue is caused by the
loss of hydrogen bonding and not by a change of
conformation.
Modifications to the thiazolium ring
The positively charged thiazolium ring of ThDP has
long been recognized as the catalytic centre of the
coenzyme [4]. Synthetic modifications to the thiazolium
moiety (Fig. 5) have been instrumental in providing
insights into the catalytic mechanism of ThDP as well
as providing information on how reaction intermedi-
ates of the coenzyme are stabilized by the various
ThDP-dependent enzymes [17,18].
Modifications at C-2
Substituents at the C-2 position of ThDP can lead to
potent inhibitors of ThDP-dependent enzymes. Two
such compounds are thiamin 2-thiazolone diphosphate
(ThTDP), in which the C2–H has been replaced by
C=O, and thiamin 2-thiothiazolone diphosphate
(ThTTDP), in which the C2–H is replaced by C=S
Fig. 3. Modifications to the aminopyrimidine ring of ThDP.
Fig. 4. Amino acid residues surrounding ThDP in PDH E1 from
Escherichia coli (from PDB entry 1L8A). The carbons of ThDP are

in green and other carbons in grey. Conserved glutamate residue
Glu571 hydrogen bonds to N
1
0
of ThDP. Figures were drawn using
PYMOL [59].
K. Agyei-Owusu and F. J. Leeper Studies with analogues of thiamin diphosphate
FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS 2907
[18]. Both are tight binding but reversible inhibitors of
the E1 component of PDH of Escherichia coli.
ThTDP, in particular, was found to have a K
i
value in
the very low nm range, as measured by a number of
methods. It can be seen that both ThTDP and
ThTTDP mimic the neutral enamine intermediate com-
mon to all ThDP-dependent enzymes and, as such, it
is not surprising that they bind tightly to the enzyme.
An interesting result obtained from studying these two
analogues was the discovery of a new positive CD
band at 330 nm when ThTTDP is added to the E1
component of PDH [18], which is absent when either
ThDP or ThTDP is added to the subunit. This phe-
nomenon is thought to be caused by the chiral confor-
mation imposed on ThTTDP when it is bound in the
active site. 2-Methyl-ThDP was also found to inhibit
the enzyme by preventing formation of the ThDP com-
plex [9]. Several structures of ThTDP bound to ThDP-
dependent enzymes have been solved, including human
branched-chain 2-keto acid dehydrogenase (Protein

Database [PDB] entries 2BFC and 2BFF), benzoyl-
formate decarboxylase (1YNO), oxalyl CoA decarbox-
ylase (2C31) and PDH E1 (1RP7). In the last of these
examples, the tighter binding of ThTDP than ThDP
was ascribed to an increase in the number of hydrogen
bonds between the protein and the ligand [19].
A further derivative of ThDP modified at C-2 is
tetrahydroThDP 2, which is formed by reduction of
ThDP with sodium borohydride. TetrahydroThDP is
reported to inhibit yeast TK with a K
i
value of 0.4 lm
[20], yeast PDC with a K
i
value of 6.5 lm [21] and
PDH complex with an IC
50
of 0.046 lm [22]. Tetra-
hydroThDP made by sodium borohydride reduction of
ThDP consists of two racemic diastereoisomers. The
diastereoisomers have been separated and it was
found that the cis isomer was a much more potent
inhibitor (K
i
= 0.02–0.15 lm) than the trans isomer
(K
i
= 5–10 lm) [23].
Structures representing the pre-decarboxylation stage
of the reaction of PDH E1 [24–25] and pyruvate oxi-

dase [26] have been obtained by incubating the native
enzyme with methyl acetylphosphonate. This reacts
with the ThDP ylid to produce 2-phosphonolactyl-
ThDP, an analogue of 2-lactyl-ThDP (Fig. 2) that has
-PðOMeÞO
À
2
in place of -CO
À
2
. Similarly, reaction of
benzaldehyde lyase with methyl benzoylphosphonate
produces a phosphonate analogue of 2-mandelyl-ThDP
[27]. Interestingly with benzoylformate decarboxylase,
if benzoylphosphonate is used instead of its methyl
ester, a phosphoryl group transfer occurs to an active-
site serine residue [28]. Succinylphosphonate and its
monoethyl esters, inactivate a-ketoglutarate dehydro-
genase [29], so presumably this also forms phosphono
analogues of the predecarboxylation intermediate,
though in this case no crystal structure has been
reported as yet.
3-Deazathiamin diphosphate and derivatives
Among the most potent inhibitors of ThDP-dependent
enzymes is 3-deazathiamin diphosphate (3-deazaThDP)
3, first synthesized by Hawksley et al. (Fig. 6) [30,31].
In this compound, a carbon atom replaces the N-3
Fig. 6. 3-DeazaThDP 3 and its derivatives 4 and 5, triazole ana-
logues 6 and 7, and open-chain analogues 8 and 9.
Fig. 5. Some modifications to the thiazolium moiety that have been

studied. One enantiomer of the cis isomer of tetrahydro-ThDP 2 is
shown.
Studies with analogues of thiamin diphosphate K. Agyei-Owusu and F. J. Leeper
2908 FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS
atom of ThDP resulting in a neutral thiophene ring in
place of the thiazolium ring of the coenzyme. This
analogue is of the same size and steric profile as ThDP
and the only difference is the absence of a positive
charge at the 3-position, which precludes the formation
of the reactive ylid required for catalysis. Enzymatic
studies with 3-deazaThDP carried out on PDC from
Zymomonas mobilis (ZmPDC) showed it to be an
essentially irreversible inhibitor, binding $ 25 000
times more tightly than ThDP [31]. Binding to a-keto-
glutarate dehydrogenase (EC 1.2.4.2) E1 component
by 3-deazaThDP was also found to be 500 times stron-
ger than for ThDP [31]. In both enzymes studied,
binding of the analogue occurred at a faster rate than
the natural coenzyme. Similar results have been
obtained with pyruvate dehydrogenase and branched-
chain 2-keto acid dehydrogenase E1 components (see
below) as well as with transketolase (K. M. Erixon &
F. J. Leeper, unpublished results).
It is initially surprising to find that 3-deazaThDP
binds much tighter than the natural coenzyme. The
key to rationalizing this result is to note that it is a
good mimic of the ylid structure in which the five-
membered ring is neutral overall. As a consequence of
the charge being reduced from +1 to neutral, there is
an increase in hydrophobic interactions between the

enzyme’s active site residues and the analogue, which
in turn leads to tighter binding. It has been shown that
the enzyme stabilizes the neutral ylid and enamine
intermediates in the catalytic cycle by providing an
active site of low dielectric constant [32]. This would
assist the formation of these neutral intermediates
from their charged precursors.
In studies on PDH E1, it was found that the protein
displays half-of-sites reactivity towards proteolysis of
the active-site loops when ThDP is bound but is pro-
tected from cleavage at both active sites of the a
2
b
2
tetramer when 3-deazaThDP is bound. This observa-
tion led to the ‘proton-wire’ hypothesis in which com-
munication between the active sites is mediated by the
shuttling of a proton down a solvent-filled tunnel that
connects the two active sites [33].
3-DeazaThDP has also been used to obtain crystal
structures of the ThDP-dependent enzymes with their
substrates bound. In most cases, equivalent structures
with ThDP bound could not be obtained because the
reaction occurs too quickly. Thus, the structure of a
complex of oxalyl CoA decarboxylase with 3-dea-
zaThDP and oxalyl CoA was solved and this revealed
both the CoA binding site and the ordering of the
C-terminus of the protein to form a lid over the CoA
chain (PDB entry 2JI6) [34]. In the case of phenylpyru-
vate decarboxylase, crystallizing the enzymes with

3-deazaThDP bound allowed a structure of the enzyme
to be obtained which had substrate molecules in both
the active site and the regulatory site, thus unveiling
the mechanism of allosteric substrate activation [35].
As well as being a very potent inhibitor, 3-deaza-
ThDP has the advantage over neutral analogues such
as ThTDP in that it can be functionalized at the C-2
position in order to make very close mimics of reaction
intermediates in the catalytic cycle of various ThDP-
dependent enzymes. In so doing, very selective and
potent inhibitors of the E1 components (E1p and E1b)
of pyruvate dehydrogenase complex (PDHc) and the
related branched-chain keto acid dehydrogenase com-
plex (EC 1.2.4.4) have been produced (M. D. H. Wood
and F. J. Leeper, unpublished results). PDHc and
branched-chain 2-keto acid dehydrogenase complex
belong to the highly complex 2-oxoacid dehydrogenase
family of enzymes. Enzymes in this family have a
molecular mass of between 4 and 10 · 10
6
Da. PDHc
comprises three different enzymic components (E1, E2
and E3) that work in tandem to catalyse the oxidative
decarboxylation of pyruvate to give acetyl CoA, CO
2
and NADH as products (Fig. 7). This is carried out
with the aid of no fewer than five coenzymes, namely
ThDP, CoA, lipoic acid, NAD
+
and FAD. The first

reaction catalysed by PDHc is the ThDP-dependent
decarboxylation of pyruvate by the E1 component, an
a
2
b
2
heterotetramer with two active sites located at the
interfaces between the a- and b-subunits [33].
3-DeazaThDP proved to be a potent inhibitor of
both E1p and E1b with K
i
values of 0.14 and 0.48 nm,
respectively. For comparison, ThDP has a K
D
for both
E1 components of $ 3 lm. The time-course of the
inactivation of the holoenzyme is relatively slow,
because of the slow rate of unbinding of ThDP. It was
observed that there is a faster initial rate of inactiva-
tion followed by a much slower rate. This was
observed for both enzymes although it is more pro-
nounced for E1b. This profile may be evidence for the
already mentioned half-of-sites reactivity. The two
active sites of the E1 component are in alternate
Fig. 7. Overall reaction catalysed by the pyruvate dehydrogenase
complex.
K. Agyei-Owusu and F. J. Leeper Studies with analogues of thiamin diphosphate
FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS 2909
conformational states, with one being ‘open’ and the
other ‘closed’. The more rapid phase of the inactiva-

tion may be caused by binding of the inhibitor after
ThDP has unbound from the ‘open’ conformation,
whereas the slow phase may be caused by binding of
the second molecule of inhibitor in the second active
site, which has to change from a ‘closed’ to an ‘open’
conformation to allow its ThDP to unbind.
Analogues 4 and 5 (Fig. 6) synthesized readily from
3-deazathiamin by Friedel–Crafts acylation at the C-2
position, followed by reduction of the ketone and
pyrophosphorylation, proved to be even better inhibi-
tors for their corresponding E1 components than
deazaThDP (Fig. 5). 4 closely mimics the enamine
reaction intermediate of the E1p reaction, whereas 5
mimics the enamine intermediate of E1b. For the E1p
component, analogue 4 showed excellent affinity with
a K
i
value of 0.1 nm. Analogue 5, by contrast, showed
no detectable inhibition, thus confirming that the E1
component of PDHc shows a high degree of selectivity
for its natural substrate pyruvate over branched-chain
keto acid substrates. The opposite is true for the E1b
subunit in which analogue 5 binds with a higher affin-
ity (K
i
= 0.17 nm) than 4 (K
i
= 0.44 nm). The fact
that 4 binds with less affinity can be attributed to its
shorter methyl side chain which would have fewer

hydrophobic interactions with the enzyme compared
with the longer branched side chain.
The selectivity of both E1 components for the R and
S enantiomers of 4 and 5 was also probed. Interest-
ingly neither enzyme shows any preference for either
enantiomer of 4 but E1b shows a three- to four-fold
preference for binding the R enantiomer of 5.
Crystal structures have been obtained of 4 bound in
the ThDP-binding sites of phenylpyruvate decarboxy-
lase [35] and the branched-chain keto acid decarboxy-
lase from Lactococcus lactis [36]. These structures
have helped define the conformations that the enzymes
would adopt when the reaction mechanisms have
reached the enamine intermediates. Using 3-dea-
zaThDP and its substituents, as well as the phosphono
analogues mentioned above, crystal structures can now
be obtained that represent ‘snapshots’ of ThDP-depen-
dent enzymes at almost every stage of the reaction.
Other synthetic analogues
The synthesis of 3-deazaThDP is a 12-step procedure
which, although producing good yields, is difficult and
time-consuming. Two inhibitors with marginally less
potency than 3-deazaThDP but which can be obtained
much more easily in four synthetic steps are the triaz-
ole analogues 6 (K
i
=20pm) and 7 (K
i
=30pm
against ZmPDC) (Fig. 6) [37]. A disadvantage of these

triazole compounds is that they cannot be functional-
ized at the 2-position to produce analogues of reaction
intermediates. They do, however, provide a readily
accessed scaffold for synthesizing mimics of the
diphosphate moiety and this is discussed in the follow-
ing section.
Having established that neutral analogues of the
thiazolium moiety such as 3-deazaThDP bind with a
much higher affinity than the natural coenzyme and
knowing that the diphosphate group is the most
important group for binding strength, we wondered if
‘open-chain’ analogues such as 8 and 9 would show
any potency as inhibitors (Fig. 6). The ‘open-chain’
analogues have the advantage of being much more
readily synthesized than their thiophene-containing
counterparts. Initial results from affinity studies
with apo-ZmPDC suggest K
i
values in the nm range
(K. Agyei-Owusu & F. J. Leeper, unpublished results).
These analogues are not expected to have the potency
of 3-deazaThDP because of their higher degree of con-
formational freedom, but they are readily synthesized
and easily functionalized into mimics of reaction inter-
mediates and, with potential K
i
values in the nm range,
show much promise as selective ThDP-dependent
enzyme inhibitors.
ThDP analogues formed during crystallization or

X-ray irradiation
In several cases, the crystal structures of ThDP-depen-
dent enzymes, once solved, have revealed that the thia-
zolium ring of the ThDP has degraded, presumably by
hydrolysis. Examples include Zm PDC (PDB entry
1ZPD) and carboxyethylarginine synthase (PDB entry
2IHU), where C-2 has been lost altogether, and both
yeast and Arabidopsis thaliana acetohydroxyacid syn-
thases in complex with herbicides such as metsulfuron
methyl (e.g. PDB entries 1YHY and 1T9D), in which
the ethyl pyrophosphate side chain appears to have
become detached from the pyrimidine ring with at
most fragments of the thiazolium ring remaining. It is
worth noting that hydrolysis of the thiazolium ring of
ThDP generates open-chain neutral species similar to 8
and 9. In view of the fact that the enzymes bind neu-
tral species more tightly than positively charged ones,
it is reasonable to assume that the enzyme causes the
hydrolysis reaction to be more thermodynamically
favourable.
In Klebsiella pneumoniae acetolactate synthase, the
structure obtained after soaking the crystals with pyru-
vate appeared to show a 2-(1-hydroxyethyl)ThDP
which had cyclized from the 4¢-amino group to C-2 to
Studies with analogues of thiamin diphosphate K. Agyei-Owusu and F. J. Leeper
2910 FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS
give a dihydrothiachrome derivative (PDB entry
1OZG). Pyruvate ferredoxin oxidoreductase is an
anaerobic enzyme that is inactivated by exposure to
both pyruvate and air. The structure of this inactive

complex shows electron density for a noncovalently
bound pyruvate molecule and an additional atom
apparently attached to the 4¢-NH
2
(PDB entry 2C3U).
It was suggested that hydroxylation of this amino
group has occurred to give the hydroxylamine [38].
Diphosphate group mimics
The diphosphate group of ThDP forms the most
important binding interactions with the enzyme by
coordinating to Mg
2+
[9]. It has been shown that inor-
ganic diphosphate on its own will compete with the
coenzyme for its active site. ThDP binds at the inter-
face of two subunits of the enzyme, with the diphos-
phate group bound to one subunit and the
aminopyrimidine moiety bound in a cavity between the
two subunits. In order to synthesize potential drug
molecules with good pharmacokinetic profiles based
on ThDP, it would be essential to make mimics of the
diphosphate group that are not as highly charged but
which retain good affinity to the enzyme. Because of
its high charge, the diphosphate group would make it
difficult for an analogue to penetrate the lipid mem-
branes of cells with consequent poor uptake and bio-
availability. With this in mind, a number of analogues
of ThDP have been synthesized with isosteres of the
diphosphate group (Fig. 8) [37].
As mentioned above, the triazole analogues of

ThDP can be readily accessed and show high affinity
to the enzyme PDC. Several analogues of the triazole
diphosphate 7 have been prepared and provide more
evidence for the critical role of diphosphate in binding.
For example, there is a difference in binding to
ZmPDC between the diphosphate 7 and its alcohol
precursor of the order of 1 · 10
7
. The general trend
observed in binding studies with the diphosphate mim-
ics was a decrease in affinity with decreasing anionic
charge. The methylene diphosphonates 10 and 11,
which are trianionic, show good binding affinity rela-
tive to the other diphosphate mimics studied, with K
i
values only $ 30–40 times greater than that of 7.
There is a successive decrease in affinity going from 10
and 11 (trianionic) to the phosphoramidic analogue 12
(dianionic), to carbamate 13 and malonate 14 (mono-
anionic), to the iminodiacetate analogue 15, for which
no binding was observed.
Pyrithiamin, riboswitches and thiamin
pyrophosphokinase
Pyrithiamin (Fig. 9) was first synthesized in 1941 by
Tracy and Elderfield [39], the culmination of efforts by
a number of groups to produce the pyridinium isostere
of the thiazolium moiety in ThDP. A 0.5 mg dose of
this analogue was found to be lethal when adminis-
tered to a newly weaned mouse, whereas a 0.17 mg
dose retarded growth in the mouse [40]. Over the

years, it has been used to produce symptoms of thia-
min deficiency in mice [41] and has been shown to be
toxic to species of fungi, algae and bacteria [42–44]. In
enzymatic studies, pyrithiamin diphosphate was found
to be only a modest inhibitor of apo-TK
(K
i
= 110 lm) [20] and apo-PDC (K
i
=78lm) [21],
which suggested that its antithiamin effects were not
the result of competition with ThDP for binding to the
enzymes. Moreover, a number of organisms that bio-
synthesize thiamin and would be expected to upregu-
late its production in the presence of pyrithiamin were
found to be unable to do so [43]. As far back as 1976,
Fig. 8. Diphosphate mimics based on the triazole analogue of
ThDP.
Fig. 9. Structures of pyrithiamin and amprolium.
K. Agyei-Owusu and F. J. Leeper Studies with analogues of thiamin diphosphate
FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS 2911
pyrithiamin was shown to disrupt the regulatory mech-
anisms of thiamin biosynthesis, causing a decrease in
thiamin production, although the underlying mecha-
nism for this phenomenon remained unknown.
The effects of pyrithiamin on microorganisms at the
molecular level became clearer with the discovery of
ThDP riboswitches [7]. Riboswitches (Fig. 10) are ele-
ments of mRNA that form receptors for a specific
ligand which, when bound, controls expression of the

gene(s) encoded in the mRNA. A number of different
classes of riboswitches have been discovered, each class
named after its specific ligand. ThDP riboswitches are
generally sited upstream of the genes coding for the
enzymes involved in thiamin biosynthesis, transport
and the salvaging of precursors to the thiazole and
pyrimidine moieties of ThDP. Depending on the organ-
ism, they can, when bound to their ligand, act either as
terminators of transcription (e.g. in Bacillus subtilis)or
as inhibitors of translation (by masking the ribosome
binding site, e.g. in E. coli) or to cause mis-splicing of
the RNA (in eukaryotes) resulting in premature termi-
nation of translation or instability of the mRNA [45].
It has been shown that pyrithiamin is taken up into
cells by thiamin transporters and pyrophosphorylated
by the enzyme TPK before binding to the ThDP ribo-
switch. Pyrophosphorylation of pyrithiamin by TPK
has also been carried out in vitro [46]. On binding of
pyrithiamin diphosphate to the riboswitch, the conse-
quent reduction in the levels of thiamin biosynthetic
enzymes leads to the depletion of intracellular thiamin
levels, preventing cell growth. Pyrithiamin-resistant
mutants of the bacteria B. subtilis and E. coli [43], the
fungus Aspergillus oryzae [47] and the alga Chlamydo-
monas reinhardtii [44] have all been characterized and
in each case it turns out that the mutation is in a
ThDP riboswitch. This causes the corresponding
biosynthetic gene(s) to be constitutively expressed, no
longer under the control of the riboswitch.
Three separate groups have obtained crystal struc-

tures of ThDP riboswitches, two using the ThiM ribo-
switch from E. coli [48,49] (Fig. 10) and one a
riboswitch from Arabidopsis thaliana [50]. Two sepa-
rate domains (P2 ⁄ P3 and P4 ⁄ P5) recognize the amino-
pyrimidine and diphosphate moieties of ThDP,
respectively. Binding of ThDP brings these two
domains together and causes the helix P1 to form,
which is what ultimately controls expression of the
gene(s). Interestingly, it appears that there is little
binding of the thiazolium moiety of ThDP and this
provides scope for the development of analogues of
the coenzyme that can interact with the riboswitch. In
the case of the E. coli riboswitch, crystal structures
were obtained with ThDP analogues thiamin mono-
phosphate, benfotiamine and pyrithiamin bound [49],
whereas for the A. thaliana riboswitch structures were
solved with oxythiamin diphosphate and pyrithiamin
diphosphate as ligands [50].
It is known that several types of antibiotics act by
binding to ribosomal RNA [51]. Riboswitches likewise
have well-defined and conserved 3D structures and so
pose attractive targets for the design of drug mole-
cules, particularly as they do not, as far as is known,
occur in animals [45].
ThDP-dependent enzymes as drug
targets
Despite the essential nature of ThDP-dependent
enzymes and the existence of several enzymes that
A
B

Fig. 10. (A) Secondary structure of the ThiM riboswitch from
Escherichia coli. Conserved nucleotides are shown in red and
conserved secondary structure in blue. Helices are labelled P1 to
P5. (B) Structure of the ThDP-binding site (from PDB entry 2HOJ).
Studies with analogues of thiamin diphosphate K. Agyei-Owusu and F. J. Leeper
2912 FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS
occur in microorganisms but not in animals, inhibitors
of ThDP-dependent enzymes have not yet found use
as antibacterials. However, it has been found that
three separate classes of herbicides (including metsulfu-
ron-methyl; Fig. 11), which had been in use for many
years, all act by inhibiting acetohydroxyacid synthase,
the first enzyme in branched-chain amino acid biosyn-
thesis. Crystal structures of these herbicides bound to
acetohydroxyacid synthase have been obtained and
show that they do not bind in the ThDP-binding site
but instead bind in the mouth of the active site, block-
ing access to the ThDP [52]. Clomazone is a commer-
cially available herbicide that acts by interfering with
terpene biosynthesis. Only relatively recently has it
been shown to act by inhibiting deoxyxylulose 5-phos-
phate synthase, the first enzyme of the non-mevalonate
pathway to terpenes [53]. However the inhibitor is not
clomazone itself but a metabolite 5-ketoclomazone.
Amprolium (Fig. 9) is a relative of pyrithiamin and
is widely used for the treatment or prevention of coc-
cidiosis in cats, dogs, poultry and cattle. It acts by
blocking thiamin uptake into cells much more effec-
tively in the parasite than in the host animal [54]. The
antibiotic metronidazole, used to treat infections by

anaerobic bacteria and protozoa, presents an interest-
ing example of a novel thiamin analogue. It turns out
that metronidazole can be a substrate for thiaminase
(which catalyses the displacement of the thiazole unit
of thiamin by various nucleophiles) to form a close
analogue of thiamin (Fig. 12) [55]. This compound
was found to inhibit thiamin pyrophosphokinase and
it is possible that the side-effects of prolonged use
of metronidazole are caused by the resulting ThDP
deficiency.
One ThDP-dependent enzyme that has gained con-
siderable attention in the last decade has been TK.
This is because it has been identified as playing an
important role in cell proliferation in a number of
tumour lines. TK is involved in the nonoxidative pen-
tose 5-phosphate pathway that leads to formation of
the ribose required for the synthesis of nucleotides
and, therefore, the expression of TK and of other
enzymes of the pathway is upregulated in cancer cells.
It has been shown both in vitro and in vivo that target-
ing TK with drugs based on ThDP leads to a decrease
in tumour growth [56]. In tests on mice, oxythiamin 16
(Fig. 13) was found to inhibit Ehrlich ascites tumour
cell proliferation by 84% at a dose of 500 mgÆkg
)1
.
The effect is enhanced when oxythiamin is adminis-
tered alongside dehydroepiandrosterone, an inhibitor
of the oxidative pentose 5-phosphate pathway, suggest-
ing that the oxidative pathway is also important.

Fig. 11. Structures of herbicides metsulfuron-methyl and cloma-
zone.
Fig. 12. Reaction of metronidazole with thiamin catalysed by
thiaminase.
Fig. 13. Structures of oxythiamin, N-3¢-pyridyl-thiamin and its disul-
fide prodrug 18.
K. Agyei-Owusu and F. J. Leeper Studies with analogues of thiamin diphosphate
FEBS Journal 276 (2009) 2905–2916 ª 2009 The Authors Journal compilation ª 2009 FEBS 2913
A large number of thiamin analogues have been syn-
thesized and tested for inhibition of TK in vitro, with
and without pyrophosphorylation by TPK, and in vivo,
as well as for their effect on tumour growth. These
analogues included both uncharged compounds like
3-deazathiamin 3 [5] and analogues with a positively
charged thiazolium ring [57]. The compound selected
for further development was the N-3¢ pyridyl analogue
17 (Fig. 13). This has poor pharmacokinetic properties
leading to rapid clearance, however, and is better
administered as its prodrug 18 [58]. (Thiamin itself has
poor oral absorption because of the low capacity of its
transporter in the gut and is often taken in similar pro-
drug form in order to treat or prevent symptoms of
thiamin deficiency.) The disulfide bond of prodrug 18
is reduced in vivo and cyclizes spontaneously to
produce 17. Both in vitro and in vivo tests on the
HCT-116 cell line showed encouraging EC
50
values for
the prodrug, which were better than those of its parent
thiazolium salt.

Concluding remarks
Enzymatic studies involving analogues of ThDP have
revealed much information on the mechanistic intrica-
cies of various ThDP-dependent enzymes. For exam-
ple, the role of hydrophobic interactions between the
enzyme and coenzyme in stabilizing reaction intermedi-
ates has become clearer, and the features of the coen-
zyme essential for binding and catalysis have been
elucidated. New and intriguing features of some
enzymes, for example, half-of-sites reactivity in the E1
component of PDH, have also been discovered. Crys-
tal structures of enzymes with analogues of reaction
intermediates bound have helped to define the roles of
the various amino acid side chains at different stages
of the reaction.
The study of thiamin and its analogues has entered
a new phase with the discovery of riboswitches and
their regulatory role in the expression of genes of the
thiamin biosynthetic pathway. This has, in turn, led to
a new set of therapeutic targets in the fight against
infections caused by pathogenic bacteria and fungi.
Analogues targeting riboswitches in these species may
be less susceptible to resistance by the target organisms
because in most cases, more than one thiamin ribo-
switch exists to regulate thiamin biosynthesis, so multi-
ple mutations would be required to achieve resistance.
Another promising area of research is the inhibition of
the enzyme TK which has been implicated in a number
of cancers. Potent inhibitors of TK continue to be
developed and this will hopefully add to the arsenal of

chemotherapeutic drugs already available.
Acknowledgements
We thank the EPSRC for a studentship to K.A O.
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