Identification of critical ligand binding determinants in Mycobacterium tuberculosis adenosine-5′-phosphosulfate reductase

Article abstract of DOI:10.1021/jm900728u

Mycobacterium tuberculosis adenosine-5′-phosphosulfate (APS) reductase is an iron-sulfur protein and a validated target to develop new antitubercular agents, particularly for the treatment of latent infection. To facilitate the development of potent and specific inhibitors of APS reductase, we have probed the molecular determinants that underlie binding and specificity through a series of substrate and product analogues. Our study highlights the importance of specific substitutent groups for substrate binding and provides functional evidence for ligand-specific conformational states. An active site model has been developed for M. tuberculosis APS reductase that is in accord with the results presented here as well as prior structural data reported for Pseudomonas aeruginosa APS reductase and related enzymes. This model illustrates the functional features required for the interaction of APS reductase with a ligand and provides a pharmacological roadmap for the rational design of small molecules as potential inhibitors of APS reductase present in human pathogens, including M. tuberculosis.

Full text of DOI:10.1021/jm900728u

J. Med. Chem. 2009, 52, 5485–5495 5485
DOI: 10.1021/jm900728u
Identification of Critical Ligand Binding Determinants in Mycobacterium tuberculosis
Adenosine-50-phosphosulfate Reductase
Jiyoung A. Hong,† Devayani P. Bhave,‡ and Kate S. Carroll*,†,‡,§
§
†Department of Chemistry, ‡Chemical Biology Graduate Program, and Life Sciences Institute, University of Michigan,
210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216
Received May 28, 2009
Mycobacterium tuberculosis adenosine-50-phosphosulfate (APS) reductase is an iron-sulfur protein and
a validated target to develop new antitubercular agents, particularly for the treatment of latent infection.
To facilitate the development of potent and specific inhibitors of APS reductase, we have probed the
molecular determinants that underlie binding and specificity through a series of substrate and product
analogues. Our study highlights the importance of specific substitutent groups for substrate binding and
provides functional evidence for ligand-specific conformational states. An active site model has been
developed for M. tuberculosis APS reductase that is in accord with the results presented here as well as
prior structural data reported for Pseudomonas aeruginosa APS reductase and related enzymes. This
model illustrates the functional features required for the interaction of APS reductase with a ligand and
provides a pharmacological roadmap for the rational design of small molecules as potential inhibitors of
APS reductase present in human pathogens, including M. tuberculosis.
1. Introduction
256 (Residue numbers throughout manuscript correspond
to the APS reductase sequence from P. aeruginosa (Figure
S1, Supporting Information) on the sulfur atom in APS to
form an enzyme S-sulfocysteine intermediate, E-Cys-Sγ-
SO3-, which is then reduced through intermolecular thiol-
disulfide exchange with thioredoxin. The iron-sulfur cluster
in APS reductase is essential for activity; however, it is
not involved in redox chemistry and its exact role remains
unknown.6,11
Reduced sulfur appears in organic compounds essential to
all organisms as constituents of proteins, coenzymes, and
cellular metabolites.1-3 In the amino acid cysteine, the thiol
functional group plays important biological roles in redox
chemistry, metal binding, protein structure, and catalysis.4 In
many human pathogens such as Mycobacterium tuberculosis
and Pseudomonas aeruginosa, activation of inorganic sulfur
for the biosynthesis of cysteine proceeds via adenosine-
50-phosphosulfate (APSa).5,6 This high-energy intermediate
isproduced bythe actionof ATP sulfurylase, which condenses
sulfate and adenosine-50-triphosphate (ATP) to form APS.1
The iron-sulfur protein, APS reductase catalyzes the first
committed step in sulfate reduction and is a validated target to
develop new antitubercular agents, particularly for the treat-
ment of latent infection.7-9
˚
Crystal structure determination at 2.7 A of P. aeruginosa
APS reductase in complex with APS provided the first insight
into the molecular basis for substrate recognition (Figure 3).12
M. tuberculosis and P. aeruginosa APS reductases are related
by high sequence homology (27.2% of sequence identity and
41.4% of sequence similarity), particularly in the residues that
line the active site. The protein monomer folds as a single
domain with a central six-stranded β sheet, interleaved with
seven R-helices (Figure 3). Opposite the nucleotide at one end
of the active site is the [4Fe-4S] cluster. Three additional
elements define the active site: the P-loop (residues 60-66),
the LDTG motif (residues 85-88), and the Arg-loop (residues
162-173). APS fits into the active site cavity with the phos-
phosulfate moiety extending toward the protein surface and
10 residues interact directly, via hydrogen bonding or hydro-
phobic interactions with the substrate. The C-terminal seg-
ment of residues 250-267, which carries the catalytically
essential Cys256, is disordered in this structure but would be
positioned above the active site cleft.
APS reductase catalyzes the reduction of APS to sulfite
2-
(SO3 ) and adenosine-50-monophosphate (AMP) using re-
duction potential supplied by the protein cofactor, thioredox-
in, as shown in Figure 1. Functional and structural studies
have been used to investigate the mechanism of APS reductase
from sulfate-assimilating bacteria.10-12 The proposed me-
chanism in Figure 2 involves nucleophilic attack by cysteine
*To whom correspondence should be addressed. Phone: 734-615-
2739. Fax: 734-764-1075. E-mail: katesc@umich.edu.
a Abbreviations: [4Fe-4S], four iron, four sulfur; TB, tuberculosis;
ATP, adenosine-50-triphosphate; AMP, adenosine-50-monophosphate;
PAPS, 30-phosphoadenosine-50-phosphosulfate; PAP, 30-phosphoade-
nosine-50-phosphate; ADP, adenosine-50-diphosphate, ADPβS, adeno-
sine-50-O-β-thiodiphosphate; ADPβF, adenosine-50-O-β-fluorodiphos-
phate; AMPCF2P, adenosine-50-O-R,β-difluoromethylenediphosphate;
AMPCP, adenosine-50-O-R,β-methylenediphosphate; AMPNP, adeno-
sine-50-O-R,β-imidodiphosphate; AMPPN, adenosine-50-O-β-amidodi-
phosphate; APSβM, adenosine-50-O-R,β-methylenephosphosulfate;
AMPS, adenosine-50-O-thiophosphate; AMPN, adenosine-50-O-amido-
phosphate.
Not all organisms that assimilate sulfate reduce APS as the
source of sulfite. Through divergent evolution, some organ-
isms, such as Escherichia coli and Saccharomyces cerevisiae,
reduce the related metabolite 30-phosphoadenosine-50-phos-
phosulfate (PAPS),10 which is produced by APS kinase from
ATP and APS.13 PAPS reductases lack the iron-sulfur
cofactor but utilize the same two-step mechanism shown in
r
2009 American Chemical Society
Published on Web 08/14/2009
pubs.acs.org/jmc

5486 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17
Hong et al.
Figure 1. Sulfate assimilation pathway in M. tuberculosis. The majority of sulfate reducing bacteria use APS as their source of sulfite. In this
reaction, APS is reduced to sulfite and adenosine-50-monophosphate (AMP) by APS reductase. Sulfite, in turn, is reduced by later enzymes in
this metabolic pathway, forming first sulfide before incorporation into cysteine and, ultimately, to methionine and other essential reduced
sulfur-containing biomolecules.
Figure 2. Mechanism of sulfonucleotide reduction.
Figure 2.10,11 S. cerevisiae PAPS reductase, crystallized in the
presence of the product, 30-phosphoadenosine-50-phosphate
(PAP),14 has a fold similar to APS reductase (1.6 A rms
˚
deviation over 117 residues). In the structure of yeast PAPS
reductase, the Arg-loop and C-terminal segment are folded
over the active site and this conformation reveals additional
enzyme-ligand contacts, which may also form between APS
reductase and its substrate, APS.
Even though M. tuberculosis has plagued humans for
millennia, the antibiotic regime is complex and effective drugs
that specifically target latent TB infection are yet to be
developed.15 Novel targets16,17 and treatment strategies18,19
are emerging, but new avenues for therapeutic intervention
must continue to be explored in order to combat multidrug-
Figure 3. Structure of P. aeruginosa APS reductase in complex with
resistant strains of TB, which pose a significant threat to
substrate, APS (PDB deposition 2GOY). The C-terminal segment
of residues starting at Glu249 carries the catalytically essential
Cys256 and is disordered.
global human health.20 To this end, APS reductase represents
an attractive target for therapeutic intervention because it is
essential for mycobacterial survival in the latent phase of TB
infection9 and humans do not possess an analogous metabolic
pathway. Recently, we have discovered small-molecule inhi-
bitors of APS reductase through virtual ligand screening.21
However, the development of more specific and potent in-
hibitors will be greatly aided through knowledge of the
functional importance of interactions between the substrate
and enzyme at the active site, which have not yet been
experimentally addressed.
for molecular recognition and reveal a network of electrostatic
interactions, which play an important role in substrate dis-
crimination. An active site model has been developed for
M. tuberculosis APS reductase that is in accord with the
results presented here as well as prior structural data reported
for P. aeruginosa APS reductase and related enzymes. This
model illustrates the functional features required for the
interaction of APS reductase with a ligand and provides a
pharmacological roadmap for the rational design of small
molecules as potential inhibitors of APS reductase present in
human pathogens, including M. tuberculosis.
Herein, we probe binding determinants of the M. tubercu-
losis APS reductase active site using synthetic ligand analo-
gues. These studies define chemical groups that are essential

Article
Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17 5487
Table 1. Ligand Dissociation Constants for Substrate Fragments with APS Reductase
a The Kd of APS was measured under single turnover conditions, in the absence of thioredoxin, as described in the Experimental Procedures. b Due to
the limits of solubility or solution ideality the reported values are lower limits. c For substrate fragments in this table values of Ki were determined under
single turnover conditions from the dependence of the observed rate constant at a given inhibitor concentration under conditions of subsaturating APS,
such that Ki is equal to the Kd. Each value reflects the average of at least two independent experiments, and the standard deviation was less than 15% of
the value of the mean. Kinetic data were nonlinear-least-squares fit to a model of competitive inhibition. d Energetic difference in affinity of APS rela-
tive to inhibitor, ΔΔG=-RT ln(KdAPS/Kdfragment). e pKa estimated from value measured for 20-deoxy-50-phosphoribose.58 f pKa estimated from value
measured for 30-phospho-50-adenosinephosphosulfate.59
2. Results and Discussion
moiety makes a substantial contribution (7.3 kcal/mol) to
the overall binding affinity (9.3 kcal/mol) of APS. Deletion
of the adenine or phosphate group from AMP decreased
binding to APS reductase by ∼170-fold (3.1 kcal/mol) and
∼550-fold (3.8 kcal/mol), respectively. Fragments of adeno-
sine, D-ribose and adenine, exhibited weak binding activity
toward APS reductase (0.2 and e1.5 kcal/mol). The respective
free energy of binding to sulfate and phosphate dianions was
e0.7 and 1.6 kcal/mol. Figure 4 summarizes the binding
properties of the substrate, APS, and product, AMP for
M. tuberculosis APS reductase, as compared with those of
the fragments obtained by cutting these ligands at seve-
ral positions, including the glycosidic bond, and at R- or
β-positions within the diester moiety. In all cases, the Kd value
of APS or AMP was lower than those of its pieces. However,
the free energies (ΔGconn) associated with these connectivity
effects for APS reductase are modest (e2.2 kcal/mol) as
compared to values that have been determined for adenosine23
and cytidine deaminases24 (∼10 kcal/mol).
The substrate and fragments studied and results obtained
in these experiments are summarized in Tables 1-3 and
Figures 4-9.
2.1. Substrate Affinity. As a starting point to explore the
molecular recognition properties of APS reductase, we de-
termined the Kd value of substrate APS for M. tuberculosis
APS reductase from the dependence of the observed rate
constant for S-sulfocysteine formation (Figure S2, Support-
ing Information), as described in Experimental Procedures.
The substrate APS binds to APS reductase with a Kd value of
0.2 μM (Table 1), which is ∼3-fold lower than the value of the
reported substrate Km.22
2.2. Affinity of Substrate Fragments. To gain further in-
sight into substrate recognition of M. tuberculosis APS
reductase, we analyzed the energetic contribution of indivi-
dual portions of APS to the enzyme-binding interaction. The
results obtained in these experiments are summarized in
Table 1. The product AMP differs chemically from the
natural substrate, APS, by the absence of the sulfate moiety.
The loss of sulfate from APS reduced binding to APS reductase
about 30-fold (2 kcal/mol), demonstrating that the AMP
2.3. Affinity of Substrate Analogues. 2.3.1. β-Nucleotide
Substitution. The results above suggest that the β-sulfate
group plays a modest role (e2.0 kcal/mol) in molecular

5488 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17
Hong et al.
Table 2. Ligand Dissociation Constants for Substrate Analogues with
APS Reductase
Table 3. Ligand Dissociation Constants for Product AMP Analogues
with APS Reductase
a For analogues in this table, values of Ki were determined under
single turnover conditions from the dependence of the observed rate
constant at a given inhibitor concentration under conditions of sub-
saturating APS, such that Ki is equal to the Kd. Each value reflects the
average of at least two independent experiments, and the standard
deviation was less than 15% of the value of the mean. Kinetic data were
nonlinear-least-squares fit to a model of competitive inhibition. b En-
ergetic difference in affinity of AMP relative to inhibitor, ΔΔG = -RT
ln(KdAMP/Kdanalogue). cpKa estimate from value measured for phosphor-
amidic acid.64
the β-position (Table 2 and Figure 5). A phosphate oxyanion
has nearly the same size and shape as a sulfate oxyanion, four
atoms arranged tetrahedrally around a sulfur instead of a
phosphorus.25,26 However, the overall charge of these analo-
gues differs because the β-sulfate is monoanionic, whereas
the β-phosphate is dianionic. Replacement of the β-sulfate
moiety with β-phosphate, as in adenosine-50-diphosphate
(ADP), diminished binding to APS reductase about 20-fold
(1.8 kcal/mol). To determine whether this decrease in binding
affinity is due to additional negative charge at the β-position of
ADP, relative to APS, we examined sulfur (ADPβS), fluorine
(ADPβF), or amine (AMPPN) substitution of the β-phosphate
nonbridging oxygen atom in ADP (Table 2 and Figure 5).
Sulfur substitution is considered to be a good mimic of the
phosphate moiety because it is isosteric, pseudoisoelectronic,
and has a similar charge distribution and similar net charge
at physiological pH.27,28 Fluorine substitution replaces an
ionizable hydroxyl group, thereby mimicking the protonated
nucleotide species in net charge at all pH values29 and, at neu-
tral pH, amine substitution neutralizes the -1 charge at the
β-position. Compared to ADP, substitution by sulfur increased
binding affinity by 2.0 kcal/mol, fluorine increased binding by
less than 2-fold (0.3 kcal/mol), and introduction of the amine
group decreased the free energy of binding for APS reductase
by 2.8 kcal/mol.
a For substrate analogues in this table, values of Ki were determined
under single turnover conditions from the dependence of the observed
rate constant at a given inhibitor concentration under conditions of
subsaturating APS, such that Ki is equal to the Kd. Each value reflects
the average of at least two independent experiments, and the stan-
dard deviation was less than 15% of the value of the mean. Kinetic
data were nonlinear-least-squares fit to a model of competitive inhi-
bition. b Energetic difference in affinity of APS relative to inhibitor,
ΔΔG=-RT ln(KdAPS/Kdanalogue). c Kd value for the diastereoisomeric
mixture of Rp and Sp isomers. d pKa estimated from value for mono- and
difluoro-substituted benzylphosphonic acid.63 epKa estimated from
effect of thio-substitution on ADPRS.61 fpKa estimated from value
measured for phosphoramidic acid.64 gpKa estimated from effect of
β-methylene-substitution on AMPCP.62
Taken together, the above data suggest that a net charge
of -2 correlates with potent enzyme-ligand interactions.
The negative charge can be localized entirely to the
R-position, as in AMP, or it can be distributed across the
recognition of APS. To probe this observation in further
detail, we investigated binding affinities for a panel of
nucleotide analogues containing systematic modifications at

Article
Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17 5489
Figure 4. Effects of cutting the substrate, APS, and the product, AMP into fragments on ligand Kd values. The energetic effect that results from
connectivity was calculated based on the affinity of the parent ligand “XY”, compared with the affinities of its pieces, “X” and “Y”: ΔGconn
=
-RT ln(KXY/KXKY), as previously reported.23
Figure 5. Electrostatic potential surfaces of substrate, APS, and related nucleotide analogues. Color gradient: red corresponds to most
negative and blue corresponds to most positive.
diester, as in ADPβF. The similarity of Kd values for AMP
and ADP could reflect different modes of nucleotide binding.
For example, the R-phosphate of AMP could occupy the
same position as the β-phosphate in ADP, thereby establish-
ing key electrostatic interactions with Lys144, Arg242, and
Arg245 (Figure 3). However, an upward shift in the position
of AMP would likely weaken important enzyme-binding
contacts with the adenine ring and ribose sugar of AMP
(Figure 3). An alternative possibility is that the C-terminus
and Arg-loop of APS reductase could adopt different
conformations, depending on whether ADP or AMP is
bound at the active site. In other words, binding energy
gained through additional charge-charge interactions be-
tween the β-phosphate moiety of ADP, Lys144, Arg242,
and Arg245 could be canceled by a decrease in favorable
interactions with residues in the C-terminus and the Arg-
loop. Evidence in support for the latter proposal is provided
in Section 5 below.
Interestingly, substitution of fluorine by an oxyanion had
a marginal effect on binding affinity, whereas thiolate sub-
stitution increased binding potency by almost 30-fold. The
larger size and polarizability of the sulfur atom could
enhance binding affinity by: (i) shortening the distance
to residues that directly contact the ligand and/or (ii) en-
abling additional electrostatic or stacking interactions with
APS reductase.30 Finally, we note that neutralizing the -1
charge of the β-phosphate, as in AMPPN, is clearly unfavor-
able. This significant energetic penalty likely results from

5490 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17
Hong et al.
Figure 6. Free energy of binding for purine and ribose-modi-
fied analogues of product, AMP. Numbers represent the ener-
getic effect of a given substitution in kcal/mol, relative to AMP
(ΔΔG = -RT ln(Kdanalogue/KdAMP). Positive ΔΔG’s indicate a
penalty for substitution.
repulsive electrostatic interactions between the amine group,
which is protonated at physiological pH (Figure 5), and
adjacent positively charged residues (Figure 3). In line with
this hypothesis, the binding affinity of AMPPN for APS
reductase increased at elevated pH (Table S1, Supporting
Information).
2.3.2. r-β Bridging Oxygen Substitution. Interactions be-
Figure 7. pH dependence for ADP (A) and AMP (B) binding. The
association equilibrium constant, (Ka=1/Kd) is plotted as a function
of pH. Values of Kd were determined by inhibition of APS reductase
(pH 6.0-9.5). Buffers were as follows: MES (pH 6.0-6.5), BisTris
(pH 6.5-7.5), TrisHCl (pH 7.5-9.5), CAPS (pH 9-9.5). See
Experimental Section for additional details. (A) The pH dependence
for ADP binding. Nonlinear-least-squares fit of the data to a model
for a single ionization gave pKa values of 6.4 ( 0.2. (B) The pH
dependence for AMP binding. The dashed line represents the best fit
of a model for a single ionization and yields a pKa of 7.9 ( 0.1.
tween the 50-phosphate and two highly conserved resi-
dues, Arg171 and His259, are observed in the structure of
S. cerevisiae PAPS reductase bound to PAP.14 However,
owing to the mobility of the Arg-loop and C-terminal resi-
dues, no direct contacts tothe R-phosphate are observedinthe
structure of APS reductase12 (Figure 3). To gain insight into
the functional importance of these contacts for M. tuber-
culosis APS reductase, we examined the contribution of the
R-β bridging oxygen to binding affinity (Table 2). Replacing
the PR-O-Sβ bridging oxygen in APS with a methylene
group (PR-CH2-Sβ) significantly decreased binding affinity
by ∼3500-fold (4.9 kcal/mol). Comparison of ADP with
AMPNP (PR-NH-Pβ), AMPCF2P (PR-CF2-Pβ), and
AMPCP (PR-CH2-Pβ) shows that imino, difluoromethy-
lene, or methylene substitutions reduced binding potency by
approximately 60-fold (2.5 kcal/mol), 3-fold (0.7 kcal/mol),
and 6-fold (1.1 kcal/mol), respectively.
able contacts to the R-β bridging position of AMPCP.
NMR studies show that AMPPNP and PNP exist in solution
primarily as the imido tautomers.33 Thus, the observed
decrease in binding affinity could be due to restricted rota-
tion about the PR-NH-Pβ bonds.
2.3.3. r-Nucleotide Substitution. Next, we examined the
effect of sulfur substitution at the R-nonbridging oxygen
atom using the analogues, APSRS and ADPRS (Table 2). (In
principle, APSRS could be utilized as a substrate by APS
reductase. However, under saturating conditions, no evi-
dence for formation of the S-sulfocysteine intermediate has
been obtained (data not shown). At present, it is not under-
stood why APS reductase does not effectively reduce APSRS.
One possible explanation is that the R-sulfur substitution
disrupts contact with residues that could be important for
stabilizing charge development in the transition state, such as
Arg171 and His259.) Comparison of APS and APSRS shows
that sulfur substitution for oxygen decreased binding by
more than 200-fold (3.2 kcal/mol). However, compared to
ADP, the binding potency of ADPRS increased by approxi-
mately 5-fold (1 kcal/mol). The larger energetic penalty for
R-sulfur substitution of APS could result from ligand-related
differences in enzyme conformation, similar to the scenario
presented in the subsection above.
The above findings demonstrate that the R-β bridging
oxygen does contribute to ligand recognition. Nonetheless,
these data pose several questions: Why is the methylene
substitution more detrimental for APS binding, relative to
the energetic penalty paid for similar modification of ADP?
And, why does AMPNP bind more weakly to APS reductase
compared to AMPCF2P? Replacing the bridging oxygen
with a methylene group decreases the S/P-X-P bond angle,
increases S/P-X bond length, increases the negative charge
density on nonbridging oxygens, but makes the phosphate
and sulfate groups less acidic.31,32 It is possible that methy-
lene substitution of ADP is less detrimental to binding
because (i) the phosphonate moiety has more torsional free-
dom, allowing the nucleotide to adopt an alternative favor-
able binding mode and/or (ii) conformational differences in
the C-terminal and Arg-loop segments minimize unfavor-

Article
2.4. Affinity of Product AMP Analogues. 2.4.1. r-Nucleo-
tide Substitution. To probe the molecular binding determi-
Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17 5491
compared the Kd value for the product, AMP, to values
measured for related analogues (Table 3). The respective
effects of substitution at the R-oxygen by sulfur (AMPS) or
amine (AMPN) are -0.3 and þ1.8 kcal/mol, compared to
AMP. The modest increase in binding energy that results
from sulfur modification is similar to the effect observed with
ADPRS. The reduction in binding affinity of AMPN also
parallels the decrease observed for AMPPN.
nants of APS reductase at the R-position in greater detail, we
In PAPS reductase, residues in the P-loop interact with the
30-phosphate of PAP.14,34 However, in APS reductase,
the acidic residue, Asp66, interacts with amide groups of
the P-loop and thus appears to mimic the interaction of
the negatively charged 30-phosphate group. To investigate
the role of the 30-hydroxyl group in ligand discrimination
(see also Section 2.4.2 below), we determined the bind-
ing affinity for 30-AMP, which reverses the position of the
50-phosphate and 30-hydroxyl groups (Table 3). Switching
the position of the phosphate moiety decreased binding by
∼600-fold (3.8 kcal/mol), indicating that, while the analogue
binds poorly, the 30-phosphate does not impact binding to
APS reductase, as compared to adenosine. By contrast,
addition of a 30-phosphate group to AMP, as in PAP,
decreased binding affinity by 3.0 kcal/mol. The energetic
penalty for 30-phosphate in PAP, but not 30-AMP, likely
reflects additional binding interactions to the 50-phosphate,
which could decrease conformational freedom and increase
unfavorable protein-ligand contacts.
2.4.2. Purine and Ribose Substitution. Next, we analyzed
the relative energetic contributions of individual purine
and ribose substitutents to the enzyme-binding interaction.
Owing to the relative difficulties traditionally associated
with the preparation of ADP analogues and the weak bind-
ing of adenosine, we determined affinities for a series of
compounds derived from the AMP scaffold. As shown in
Figure 6, energetic penalties for individual substitutions
ranged from 0.6 to 4.7 kcal/mol. First, we probed interac-
tions between the N6 amine and N1 of adenine and Leu85
(Figure 3), the first residue in the conserved LDTG motif.
Loss of the N6 amine from AMP reduced the free energy of
binding to APS reductase by 1.8 kcal/mol. Replacing hydro-
gen atoms with methyl groups at the N6 position of adenine
decreased binding affinity by 35-fold (2.1 kcal/mol) per
substitution. Inverting the hydrogen bond donor and accep-
tor, as in inosine-50-monophosphate, was also disfavored
(4.7 kcal/mol), presumably due to electrostatic repulsion
between the O6-keto and the Leu85 carbonyl, and the N1
by the Leu85 amine. Likewise, introduction of an N1 amine
markedly reduced the affinity of this analogue for APS
reductase (4.7 kcal/mol). In subsequent experiments, we
determined the binding potency of AMP analogues with
Figure 8. APS reductase interactions with substrate, APS inferred
from P. aeruginosa APS reductase (PDB deposition 2GOY) and S.
cerevisiae PAPS reductase (PDB deposition 2OQ2) structures and
functional data obtained in the present study. (A) Summary of
proposed active site contacts to APS. (B) Summary of proposed
active site contacts to APS, plotted in two dimensions. A total of
nine protein residues are shown in proximity around the ligand, with
hydrogen bonding interactions shown where detected. Hydrogen
bonds are draw as dotted lines with arrows denoting the direction of
the bond. Interactions from substrate or the residue backbones of
the enzyme are distinguished from the interactions with residue side
chains by a solid dot at the end of the interaction line. Active site
residues between P. aeruginosa and M. tuberculosis APS reductase
are largely conserved, with the exception of residues implicated in
hydrophobic interactions (Ser62 to Met67, Ser84 to Phe87, Phe61 to
Asn66). The corresponding numbers for residues conserved be-
tween M. tuberculosis and P. aeruginosa APS reductase are: Ser65
(Ser60), Leu88 (Leu85), Lys145 (Lys144), Gly162 (Gly161), Arg171
(Arg171), Arg237 (Arg242), Arg240 (Arg245) Cys249 (Cys256), and
His252 (His259). See also Figure S1 of the Supporting Information.
Figure 9. Pharmacophore model of substrate, APS. Chemical structure of APS highlighting key hydrogen bond accepting (HBA) and
donating (HBD) interactions, ionic interactions, and van der Waals interactions based on functional data obtained in the present study.

5492 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17
Hong et al.
substitutions at the 2-, 7-, and 8-positions of the purine ring.
Methylation at N2 had a detrimental effect on binding
(3.4 kcal/mol), likely due to steric clashes with the surround-
ing adenine-binding pocket (Figure 3). The structure of APS
reductase bound to APS shows that C8-H group is directed
toward the 50-phosphosulfate moiety (Figure 3). Not surpris-
ingly then, amine substitution at this position decreased the
free energy of binding by 3.7 kcal/mol. No contacts are
formed between N7 and APS reductase (Figure 3). Consis-
tent with this observation, replacing N7 with a carbon atom
had a relatively minor effect on binding affinity (0.6 kcal/mol).
Finally, we investigated the influence of modification at the
20- and 30-hydroxyl groups of the ribose sugar. 20-deoxy
and methoxy group substitutions reduced the free energy of
binding by a respective 4.0 and 3.6 kcal/mol, whereas 30-deoxy
substitution had only a modest effect on binding affinity
(0.9 kcal/mol). This indicates that hydrogen bonds between
the 20-hydroxy group and Ser60 and Gly161 residues (Figure 3)
play a vital role in substrate recognition.
2.5. pH Dependence of Ligand Binding. The pH depen-
dence for ligand binding provides information about the
relative affinities of the different nucleotide ionization states
and thus provides information about the active site environ-
ment. Initially, we investigated the pH dependence for APS
binding. However, the substantial increase in reaction rate at
higher pH precludes measurement by conventional kinetic
methods (data not shown). As an alternative, we determined
the affinities of APS reductase for the substrate analogue,
ADP, and product, AMP, as a function of pH to investigate
whether ionizations at R- and β-positions are important for
binding affinity (Figure 7). The pH dependence for ADP
binding is best fit by a pKa of 6.4 ( 0.2, which could reflect
ionizations of the free enzyme and ligand (Figure 7A). The
most likely candidate for this ionization is the ligand, as the
second pKa values of phosphate esters fall in this region.35 If
this were true, the pH profile would be expected to shift to
lower pH for an ADP analogue with lower pKa values. To
test this, we determined the pH dependence for ADPβS,
which differs in its respective pKa value by approximately
one pH unit.27 The pH dependence for ADPβS binding is
best fit by a pKa of 5.8 ( 0.2 (Figure S3A, Supporting
Information). The dependence of the pKa upon the identity
of the ligand suggests that deprotonation of the ligand is
responsible for the increase in binding at higher pH.
The pH dependence for AMP binding is best fit by a pKa of
8.1 ( 0.1 (Figure 7B), which could reflect ionizations of the
free enzyme and ligand, as described above. The simplest
model to explain the weaker binding of AMP below pH 8 is
that the dianion binds more tightly than the monoanion.
However, the apparent pKa for AMP differs from the
expected pKa of 6.8 by more than one unit. The discrepancy
between the experimental data and the simplest model is
most likely due to concurrent ionization of the enzyme that
affects ligand binding, leading to shift in the apparent pKa of
AMP. One model that could account for this upward devia-
tion is that an enzymatic group with a pKa of ∼6 contributes
slightly (∼5-fold) to AMP binding when protonated. The
most likely residue to exert such an effect on ligand binding is
His259, which interacts with the 50-phosphate of PAP in
the structure of S. cerevisiae PAPS reductase.14 Because
a stimulatory effect is not observed for ADP binding, the
C-terminal segment containing His259, and possibly the
Arg-loop, may adopt different conformations depending
on whether ADP or AMP is bound at the active site. To fur-
ther confirm that the apparent pKa measured for AMP
depends upon the identity of the ligand, we measured the
pH dependence for AMPS binding (Figure S3B, Supporting
Information). The resulting data are best fit by a pKa of
7.7 ( 0.1. The downward shift in apparent pKa suggests that
deprotonation of the ligand is responsible for the increase in
binding at higher pH.
The observed pH dependence for ADP and AMP binding
indicates that the dianion binds more tightly to APS reduc-
tase than the monoanion. These data seemingly contradict
our earlier comparison between ADP and ADPβF, whose
net charges differ by one unit but bind to APS reductase with
similar affinity (Table 2 and Figure 5). Indeed, fluorine
modification is often used to determine whether binding of
mono- or dianionic phosphate is favored.36 However, hydro-
xyl and fluorine groups are distinguished by unique chemical
properties. For example, the high electron density of fluorine
gives rise to the ability to act as an acceptor in hydrogen
bonds.37 By contrast, the hydroxyl group is a strong dipole,
with spatially separated partial positive and negative charges
that can donate as well as accept hydrogen bonds (Figure 5).
Hence, the weaker binding observed for the monoanion may
not reflect a loss of charge-charge interactions but rather an
energetic penalty that results from unfavorable charge-
dipole interactions with the hydroxyl group.
2.6. Effect of Mg2þon Ligand Affinity. In the absence of
metal ions, APS binds ∼20-times tighter to APS reductase,
compared to ADP and AMP. However, the cellular concen-
trations of these nucleotides are higher than APS38 and thus
raise an important question: How does APS compete against
binding of ADP or AMP to the active site of APS reductase
in the cell? For the majority of biochemical reactions using
ATP and related nucleotides, the active species is the Mg2þ
complex rather than the free nucleotide.39 To gain insight
into ligand discrimination by APS reductase in vivo, we
measured the Kd values for APS, ADP, and AMP in the
presence of Mg2þ. These studies show that the Kd value of
APS was independent of Mg2þ concentration (data not
shown). This observation is consistent with weak formation
constants of APS with Mg2þ40 and the general observation
that other sulfonucleotide binding enzymes, such sulfoki-
nases and sulfotransferases, also do not require Mg2þ as a
cofactor.11 However, Mg•ADP and Mg•AMP complexes
bind approximately 5-6 times weaker to APS reductase as
compared to the free nucleotide (Table S2, Supporting
Information). The observed reduction in binding energy is
most likely due to repelling interactions with multiple posi-
tively charged amino acids in the enzyme active site, such as
Lys144, Arg242, and Arg245 (Figure 3). Together, these
findings indicate that APS reductase discriminates against
noncognate adenosine nucleotides through favorable inter-
actions with the sulfate moiety of APS and by disfavoring the
binding of Mg2þ-nucleotide complexes.
2.7. Implications for Rational Inhibitor Design. Given that
APS reductase is essential for mycobacterial survival during
persistent infection,9 small-molecule inhibitors of APS re-
ductase might be a source for new drugs to treat latent
tuberculosis infection. The increasing number of antibiotic-
resistant strains suggests that the availability of such com-
pounds could play an important role in treating the disease
and minimizing the negative impact on human health. By
defining chemical groups that are essential for molecular
recognition, the work described here sets the stage for the
development of such drugs. Figure 8 summarizes the net-

Article
Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17 5493
work of interactions predicted to occur between APS reduc-
tase active site residues and substrate, APS. The structural
model was constructed by homology to S. cerevisiae PAPS
reductase14 and systematically tested in the present study
from the perspective of the ligand. The total binding energy
of APS resulting from these collective interactions is 9.3 kcal/
mol, and our data indicate several features that are essential
for optimized substrate and inhibitor binding. The hydro-
phobic adenine-binding pocket, pyrimidine ring, 20-hydro-
xyl, and the R-position are the main determinants for strong
target affinity (Figure 9). The significant losses of binding
affinity that are found to result from apparently minor
structural modifications of ligands at these key positions
have encouraging implications for inhibitor design and
suggests that, in some cases, the potency of a weak inhibitor
might be greatly enhanced by one or two simple modifica-
tions. Our studies also suggest that small molecules that
target dynamic elements within the active site, particularly
Arg171, Cys256, and His259, may lead to inhibitors with
improved binding affinity. Alternatively, molecules that trap
an inactive, “open” conformational state of APS reductase
may also represent new opportunities for inhibitor design.16
N6, N6-dimethyl-50-phosphoadenosine, N6-methyl-50-phos-
phoadenosine, 8-amino-50-phosphoadenosine, 1-methyl-50-
phosphoadenosine, and 2-amino-50-phosphoadenosine) were
synthesized by chemical phosphorylation of the correspond-
ing adenosine analogue, followed by purification via reversed
phase HPLC. Nucleosides were phosphorylated by reaction
of nucleoside with POCl3 as described.49 The nucleoside
(0.15 mmol) was suspended in triethylphosphate at 0 °C
(0.65 mL). Water (1 equiv) was added to the reaction. Subse-
quently, POCl3 (3-5 equiv, 42-70 μL) was added over a
period of 30 min with constant stirring. The suspension was
kept stirring for an additional 1.5 h, when the white suspen-
sion became a clear solution. Water (1 mL) was added to
hydrolyze the phosphoryl chloride and terminate the reac-
tion. The pH was neutralized to ∼7 by dropwise addition of
1 M NH4OH. The reaction was passed over a 2 g C18 SPE
column (Fisher) that was conditioned in acetonitrile (6 mL)
followed by H2O (6 mL). The nucleotide was eluted from the C18
SPE column with H2O. Nucleotides were purified by reversed
phase HPLC employing isocratic separation in 20 mM ammo-
nium acetate, pH 7, on a semipreparative (10 ꢀ 25 cm) C18
column, and the solvent was removed from the solution by
repeated lyophilization. The physical and spectral data for
these analogues (confirmed by 1H, 13C, and 31P NMR and
mass spectrometry) were consistent with those previously
reported for these compounds.49-51 The purity (g95%) was
confirmed by HPLC analysis using the conditions described
above. The retention time of each nucleotide analogue (N6,
N6-dimethyl-50-phosphoadenosine, N6-methyl-50-phosphoa-
denosine, 20-methoxy-50phosphoadenosine, 20-deoxy-50-phos-
phoadenosine, 8-amino-50-phosphoadenosine, 1-methyl-50-
phosphoadenosine, and 2-amino-50-phosphoadenosine) was
19.7, 19.6, 8.5, 6.1, 4.4, 4, and 3.5 min, respectively. The
concentrations of nucleotide analogues was determined by
3. Experimental Procedures
3.1. Materials. Adenosine, 2-aminoadenosine, 30-deoxyade-
nosine, 20-deoxyadenosine, 1-methyladenosine, and inosine-50-
O-monophosphate were purchased from Sigma. 50-Phosphor-
ibose, 30-phosphoadenosine, 3050-diphosphoadenosine, adenine,
and ribose were also purchased from Sigma. 7-Deazaadenosine-
50-O-monophosphate and purine riboside-50-O-monopho-
sphate were from Biology Life Science Institute. Purchased
nucleosides and other analogues were of the highest purity
available (g95%) and were used without further purification.
Additional reagents and solvents were purchased from Sigma or
other commercial sources and were used without further pur-
ification.
3.2. General Synthetic Methods. Reactions that were moisture
sensitive or using anhydrous solvents were performed under a
nitrogen or argon atmosphere. Analytical thin layer chroma-
tography (TLC) was performed on precoated silica plates
obtained from Analtech. Visualization was accomplished with
UV light or by staining with ethanolic H2SO4 or ceric ammo-
nium molybdate. Nucleosides were purified by flash chroma-
tography using Merck silica gel (60-200 mesh).
absorbance at 260 nm, assuming ε260 =15400 M-1 cm-1 52
.
3.5. Enzyme Purification. Purification of APS reductase was
carried out as previously described.10
3.6. General Kinetic Methods. 35S-labeled APS was synthe-
sized and purified as previously described10 with the inclusion of
an additional anion exchange purification step on a 5 mL FFQ
column (GE Healthcare) eluting with a linear gradient of
ammonium bicarbonate, pH 8.0. The reduction of APS to sulfite
and AMP was measured in a 35S-based assay as previously
described.53 Reactions were quenched by the addition of char-
coal solution (2% w/v) containing Na2SO3 (20 mM). The
suspension was vortexed, clarified by centrifugation, and an
aliquot of the supernatant containing the radiolabeled sulfite
product was counted in scintillation fluid. APS reductase activ-
ity was measured in single turnover reactions, with trace
amounts of 35S-APS (∼1 nM) and excess protein. These reac-
tions can typically be followed to g90% completion (Figure
S4A, Supporting Information), and the reaction time courses fit
well to eq 1, in which Frac P is the fraction product, k is the
observed rate constant, and t is time:
3.3. Preparation of Nucleoside and Nucleotide Analogues. N6,
N6-Dimethyl-50-adenosine was prepared from inosine by the
procedure described by Veliz and Beal41 and purified by flash
chromatography developed in 60:40 ethyl acetate:hexanes.
N6-Methyl-50-adenosine was prepared via reaction of 6-bromoi-
nosine with methylamine as previously described.42 8-Aminoade-
nosine was prepared by selective bromination of adenosine at the
C8 position, exchange of bromine for azide, followed by reductive
hydrogenation to afford the amine, as previously described.43
20-Methoxyadenosine was prepared from adenosine by reaction
with methyl iodide under alkaline conditions as previously
described.44 Adenosine-50-O-R,β,-imidodiphosphate (AMPNP)
was synthesized by reaction of 50-tosyladenosine45 with imidodi-
phosphate salt.45,46 Adenosine-50-O-R,β-difluoromethylenedi-
phosphate (AMPCF2P) was prepared by coupling 50-tosyladeno-
sine to difluoro substituted methylenediphosphonic acid, as pre-
viously reported.45,47 Adenosine-50-O-thiophosphosulfate (APSRS)
was synthesized by reacting pyridine-N-sulfonic acid with ade-
nosine-50-O-thiopshophate (AMPS), as previously described.48
Structures and purity (g95%) were confirmed by 1H, 31P NMR,
and HPLC analysis (data not shown).
obst
FracP ¼ 1 -exp-k
ð1Þ
Unless otherwise specified, the standard reactions condi-
tions were 30 °C with 100 mM bis-tris propane at pH 7.5, DTT
(5 mM), and thioredoxin (10 μM). Kinetic data were measured
in at least two independent experiments, and the standard error
was typically less than 15%.
The affinity of APS reductase (E) for APS was determined
from the dependence of the observed rate constant for S-sulfo-
cysteine formation on protein concentration according to eq 2:
!
½Eꢁ
kobs ¼ kmax
ꢀ
ð2Þ
K1=2 þ ½Eꢁ
3.4. Nucleoside Phosphorylation. Nucleotide analogues
(20-deoxy-50-phosphoadenosine, 20-methoxy-50phosphoadenosine,
In this equation, kobs is the observed rate constant at a particular
protein concentration, kmax is the maximal rate constant with

5494 Journal of Medicinal Chemistry, 2009, Vol. 52, No. 17
Hong et al.
saturating protein, and K1/2 is the protein concentration that
provides half the maximal rate. To ensure that the chemical
step was rate-determining, reactions were performed in NaMes
(10 mM) at pH 5.5, and control experiments demonstrate that
the enzyme is stable under these assay conditions (data not
shown). Because the chemical step is rate-determining for S-sul-
focysteine formation (kst < kmax is equal to the rate constant for
the reaction of the E•APS complex, and K1/2 is equal to the
dissociation constant (Kd) of APS for APS reductase. The
concentration of active protein was determined by direct titra-
tion with a high concentration of APS (i.e., [APS] . Kd). In
theory, the binding affinity of APS could increase at physiolo-
gical pH. However, several lines of evidence argue against this
possibility. First, the pKa of the β-sulfate moiety is less than
2 and thus, at pH 5.5, the sulfonucleotide is completely ionized.
Second, the pH dependence of ADP binding (see below) reflects
the pKa of this nucleotide in solution. Finally, the Kd measured
at pH 5.5 is in line with the apparent Km value measured at
pH 8.0.22
The affinity of various ligands for APS reductase was deter-
mined by inhibition methods. The observed rate constant of the
reaction: E þ 35S-APS f products (kobs) was determined at
varying inhibitor (I) concentrations (Figure S4B, Supporting
Information), and the [I]-dependence was fit to a simple model
for competitive inhibition (eq 3). In eq 3, ko is the rate of the
reaction in the absence of analogue, and Ki is the inhibition
constant of the analogue. With subsaturating APS reductase,
Ki is equal to the equilibrium dissociation constant (Kd) of the
ligand.
Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Sac-
charomyces cerevisiae. The apparent affinity, K1/2, of APS
reductase in single turnover experiment. pH dependence for
ADPβS (A) and AMPS (B) binding. The radioactive assay for
APS reductase. This material is available free of charge via the
Internet at http://pubs.acs.org.
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½Hþꢁ
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ꢀ
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