The challenge of developing robust drugs to overcome resistance
Transcript of The challenge of developing robust drugs to overcome resistance
Drug Discovery Today � Volume 16, Numbers 17/18 � September 2011 PERSPECTIVE
feature
The challenge of developing robustdrugs to overcome resistanceAmy C. Anderson1,2, Michael P. Pollastri1,3, Celia A. Schiffer1,4,*, [email protected] and
Norton P. Peet1,5, [email protected]
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Drug resistance is problematic in microbial disease, viral disease and cancer. Understanding at the outset
that resistance will impact the effectiveness of any new drug that is developed for these disease categories
is imperative. In this Feature, we detail approaches that have been taken with selected drug targets to
reduce the susceptibility of new drugs to resistance mechanisms. We will also define the concepts of
robust drugs and resilient targets, and discuss how the design of robust drugs and the selection of
resilient targets can lead to successful strategies for combating resistance.
Feature
IntroductionDrug resistance is defined, in a clinical setting, as
the point at which administration of the drug can
no longer safely treat the disease state owing to
an induced change in the drug target or an
inability of the drug to reach the target. With an
antimicrobial agent, clinical resistance occurs
when the minimum inhibitory concentration
(MIC) of the drug, for a given microbial strain,
exceeds the concentration of drug that can safely
be administered. Resistance to a drug canarise by:
(i) mutation of the gene (or gene cluster); (ii)
acquisition of extrachromosomal DNA, or a
transposable plasmid, that carries the resistance
gene or genes; (iii) upregulation of the target or;
(iv) upregulation of an efflux mechanism.
We have recently suggested [1] an approach
for combating drug resistance which involves
the selection of resilient drug targets [2] that are
evolutionally constrained and the development
of robust drugs [3] that are less susceptible to the
development of resistance.
A drug target is likely to develop resistance if it
cannot easily tolerate change and maintain
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function. Many drug targets are enzymes.
Because these enzymes perform highly con-
strained and crucial chemical reactions, they can
represent resilient targets that are less suscep-
tible to drug resistance. However, disrupting the
therapeutic target activity is necessary but not
sufficient for developing a drug that avoids
resistance.
A robust inhibitor is one that successfully
inhibits a resilient target, and one that does not
lose effectiveness quickly owing to resistance.
Such an inhibitor could only bind to crucial
regions within the target that would be essential
for function and, thus, intolerant to change. The
use of high-resolution structures and evolu-
tionary constraints aids the design of robust
inhibitors. By choosing resilient targets and
designing robust inhibitors the Institute for Drug
Resistance (IDR) [1] proposes to focus on drug
resistance in drug design strategies, and develop
a new generation of more-effective therapeutics.
This Feature will focus on selected, potentially
resilient drug targets and describe efforts to
produce drugs with various degrees of robust-
ed. doi:10.1016/j.drudis.2011.07.001
ness for these targets in the disease areas of
cancer and bacterial and viral infections. The
highlighted drug targets include: BCR-ABL
kinase; epithelial growth factor receptor (EGFR)
kinase and platelet-derived growth factor
(PDGFR) kinase in cancer; dihydrofolate reduc-
tase (DHFR) and DNA gyrase/topoisomerase IV in
bacteria; and human immunodeficiency virus
(HIV) protease and hepatitis C (NS3/4A) protease
in viruses. Because enzymes are evolutionally
constrained to catalyze a chemical reaction, they
have the potential of being resilient targets;
however, properly identifying robust inhibitors
remains a challenge for the field.
Drug resistance in enzyme targets of
cancer
Drug resistance is now a widespread problem in
cancer and is particularly problematic with kinase
inhibitors, proteasome inhibitors [4,5] and
monoclonal antibodies [6]. Of these, kinase inhi-
bitors comprise the largest class of anticancer
agents where drug resistance has significantly
limited treatment. In this article the focus will be
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on the challenges relating to developing robust
drugs that overcome resistance to inhibitors of
the kinase domains of BCR-ABL, EGFR and PDGF.
BCR-ABL inhibitors
Gleevec1 (imatinib) shows remarkable efficacy
by achieving clinical remission in chronic mye-
loid leukemia (CML). Imatinib inhibits the con-
stitutively active kinase domain, c-Abl, of the
fusion protein BCR-ABL [7] existing in CML
patients. Evidence from biochemical and crys-
tallographic studies [8] shows that imatinib
selectively binds a unique conformation of the
activation loop in which a conserved phenyla-
lanine, a member of the Asp-Phe-Gly (DFG) trio
of amino acids, undergoes an extensive 10 A
conformational change, into what is called the
DFG-out conformation [9,10]. Imatinib binding
maintains the kinase in the inactivated state.
Interestingly, many kinases cannot adopt an
inactive conformation [11]; therefore, targeting
this state yields inhibitors with selectivity over
other kinases. Crystal structures of other kinases
in the DGF-out conformation include: KIT (mast/
stem cell growth factor receptor); Aurora A; EGFR
(covered in this article); p38 or mitogen-acti-
vated protein kinase (MAPK)14; kinase insert
domain receptor (KDR); and BRAF [9].
However, the success of imatinib was limited
because of the selection of resistant mutants.
Specifically, the BCR-ABL variant with a T315I
gatekeeper mutation in the ATP-binding site was
observed in 10–20% of CML patients after failure
of imatinib [12,13]. Consequently, there are�200follow-on inhibitors of BCR-ABL kinase [14–16].
Unfortunately, it has been difficult to develop
robust inhibitors against the mutant variant of
BCR-ABL. Two recently approved agents, dasati-
nib and nilotinib (Fig. 1a), have shown success
against imatinib-resistant CML in clinical trials.
However, the BCR-ABL1 T315I variant also confers
resistance to nilotinib and dasatanib [17–21].
Thus, the problem of resistance to this class of
inhibitors is still unsolved. Approaches that are
being taken to develop robust drugs that are
effective against resistant BCR-ABL include: (i) the
design of compounds to inhibit the mutated
enzyme; (ii) allosteric inhibitors that bind at a site
different from the ATP-binding site; (iii) inhibitors
that target other tyrosine kinases and simulta-
neously inhibit the T315I variant of BCR-ABL; and
(iv) development of other dual or multikinase
inhibitors that simultaneously inhibit the ABL and
SFK (SRC family of kinases) families [15]. The SFKs
are thought to be involved in the proliferation of
BCR-ABL1-expressing cell lines [15,16,22]. The
outcomes of these approaches will be crucial to
the successful management of CML.
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EGFR inhibitors
Because EGFR, a receptor tyrosine kinase, plays a
crucial part in cellular signaling leading to
growth, proliferation and metastasis [23–30],
some investigators believed that inhibitors of its
function would serve as leads for antineoplastic
agents. Gefitinib (Fig. 1b) was approved in 2003
for the treatment of non-small-cell lung cancer
(NSCLC) after failure of platinum-based and
docetaxel therapies, but did not significantly
improve survival [31]. In 2004 erlotinib (Fig. 1b)
was also approved for NSCLC (after failure of one
other agent) and approved in 2005 for pan-
creatic cancer in combination with gemcitabine.
Both compounds are anilinoquinazolines that
compete with ATP to bind the active site of the
EGFR tyrosine kinase; a cocrystal structure of
erlotinib bound to the EGFR tyrosine kinase [32]
reveals the details of that interaction (Fig. 2a).
Genetic evidence shows that resistance occurs
in response to gefinitib and erlotinib in EGFR
through mutation of the ‘gatekeeper’ residue
T790M [33,34], similar to mechanisms of resis-
tance that occur with mutants T315I (BCR-ABL/
imatinib [35]), T6741 (PDGFR/imatinib [36]) and
T670I (c-KIT/imatinib [37]). Interestingly, there is
evidence that the T790M mutation exists before
the initiation of therapy [34] and that cells with
the mutation are then selected during therapy.
The T790M mutation was thought to introduce
steric bulk that interfered with the binding of the
inhibitors [38]. However, crystal structures and
biochemical experiments with the EGFR T790M
and T790M/L858R variants bound to inhibitors
reveal that the T790M mutation increases ATP
affinity, especially in the context of the L858R
mutation that activates the kinase [39]. By
increasing affinity for ATP, the T790Mmutation is
considered to be a multi-drug resistant mutation
that will reduce the potency of any ATP-com-
petitive inhibitor.
The development of irreversible inhibitors
such as HKI272 (Figs 1b and 2b), which is now in
Phase II trials [33,40,41], can overcome the
effects of the T790M mutation. The irreversible
inhibitors have a Michael acceptor that forms a
covalent bond with a cysteine thiol in the active
site pocket, thus eliminating the equilibrium
condition with ATP. HKI272 has been shown to
inhibit EGFR function even in the presence of the
T790M mutation, but could be subject to resis-
tance via a C797 mutation [40].
PDGFR inhibitors
PDGFR tyrosine kinase inhibitors have been
investigated as antineoplastic agents that inhibit
angiogenesis. PDGFR inhibitors are also crucial in
treating hypereosinophilic syndrome (HES), a
disease inwhich the patient has a prolonged state
of eosinophilia that can lead to organ dysfunction
and death [36]. Some patients with this disease
respond favorably to treatment with imatinib,
because they harbor a fused Fip1-like 1 (FIP1L1)-
PDGFRa gene that generates an activated kinase.
After initial treatment with imatinib, resistance is
once again selected with the mutation of the
gatekeeper residue T674I in the kinase domain of
PDGFR. Interestingly, in an analogous fashion as
EGFR, the gatekeeper mutation in many kinases,
including PDGFR, does not exert a steric effect but
has a role in favoring an activated kinase [42].
Several compounds in different stages of devel-
opment are successful at overcoming the T674I
variant (Fig. 1c). Ki11502 [43] is a potent multi-
kinase inhibitor of PDGFRa/b and inhibits T674I as
well as KIT, KDR and FLT3. Nilotinib [44] and
EXEL0862 [45] also inhibit the growth of cells
transfected with FIP1L1-PDGFRa harboring the
T674I mutation. PKC412 (midostaurin) [36], a
natural product isolated from Streptomyces, is
reported to be an effective treatment for FIP1L1-
PDGFRa-induced disease and of imatinib-
induced resistance. Although it is still ATP-com-
petitive, PKC412 could have a different binding
mode than imatinib, making it less susceptible to
imatinib-specific resistance. Sorafenib is an inhi-
bitor of the RAF-1, B-RAF, vascular endothelial
growth factor receptor (VEGFR) and PDGFR tyr-
osine kinases and is also active against cells
harboring the T674I mutation [46]. The inhibitor
HG78501 is reported to bind kinases with the
T674I mutation [47]. A cocrystal structure of
HG78501 with Src kinase shows that the com-
pound forms a H-bond with a neighboring
methionine (Met 341 in Src), possibly explaining
how HG78501 overcomes the effects of the
mutation.
Drug resistance in enzyme targets of
antibiotics
Antibacterial agents, like antineoplastic agents,
target fast-growing proliferative cells. Although
the targets differ, the occurrence of resistance is
common to both classes of drugs and the
development of robust drugs to overcome
resistant variants is an active area of research. In
this article, we highlight efforts to develop
robust drugs against DHFR and gyrase/topoi-
somerase IV.
Dihydrofolate reductase and trimethoprim
resistance
Trimethoprim (TMP) is a potent inhibitor of
bacterial species with the essential enzyme
DHFR, which plays a crucial part in the folate
biosynthetic pathway. TMP, coadministered with
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[(Figure_1)TD$FIG]
(a)
(b)
(c)
(d)
(e)
A B C
Imatinib (Gleevec) Nilotinib
Dasitinib (Sprycel)
Gefitinib
Ki11502
Nilotinib
PCK412 (Midostaurin)
Sorafenib
Nalidixic acid Ciprofloxacin Moxifloxacin GSK299423
PfizerVertex
HG78501
Erlotinib
HKl272
Drug Discovery Today
FIGURE 1
(a) Structures of first- and second-generation BCR-ABL kinase inhibitors. (b) Structures of EGFR tyrosine kinase inhibitors. (c) Structures of PDGFR inhibitors. (d)Inhibitors that target the GyrA/ParA subunit of gyrase and/or TopoIV. (e) Benzimidazole GyrB/ParE inhibitors.
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[(Figure_2)TD$FIG]
(a) (b)
Cys 797
HKl272T290M
Drug Discovery Today
FIGURE 2
Crystal structures of EGFR (green) with bound inhibitors (purple ormagenta). (a) Erlotinib competes with ATP in the active site of EGFR; (b)HKI272 forms a covalent
link with Cys 797 to eliminate the equilibrium between inhibitor and ATP.
Drug Discovery Today
FIGURE 3
Crystal structure of moxifloxicin bound to GyrA [59].
Features
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sulfamethoxazole (SMZ), is an effective thera-
peutic agent used to treat community-acquired
methicillin-resistant Staphylococcus aureus (CA-
MRSA). However, epidemiological surveys show
that �28% of MRSA strains are TMP-resistant
[48–50]. A common resistance mechanism
involves the acquisition of one of two sets of
chromosomal mutations in the DHFR gene,
either H30N/F98Y or F98Y/H149R. Structures of
wild-type and mutant (F98Y and H30N/F98Y) S.
aureus DHFR with several novel propargyl-linked
antifolates show that the structural effects of the
resistance mutations are subtle [51,52].
Development of compounds that have more
interactions within the DHFR active site has been
the predominant strategy to overcome TMP
resistance. Iclaprim, which underwent Phase III
trials but did not continue thereafter in devel-
opment, achieved nanomolar affinity for the
wild-type and mutant enzymes and showed a
lower propensity for resistance [53]. Crystal
structures of iclaprim bound to the wild-type and
mutant enzymes show additional hydrophobic
interactions in a highly conserved area of the
substrate-binding site [54]. Reported propargyl-
based inhibitors also interact more substantially
with the active site [51,52] than TMP and are less
affected by the mutations that cause TMP
resistance; further experiments to assess their
propensity for resistance are ongoing.
DNA gyrase and topoisomerase IV
inhibitors
In Gram-negative and Gram-positive bacteria
gyrase and topoisomerase IV, respectively, are
important drug targets [55] that serve parallel
functions and are often targeted with the same
compounds. To perform the processes of tran-
scription, replication, repair and recombination,
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topoisomerases catalyze either a transient sin-
gle-strand break (Type I) or a double-strand
break (Type II) in supercoiled DNA. In bacteria,
gyrase introduces negative supercoils for the
entire chromosome, creating condensed
packages of genetic material that can be divided
correctly during cell division [56,57].
Fluoroquinolones are an established class of
drugs (Fig. 1d) that stabilize the covalent DNA-
gyrase complex and thehomologousDNA-topoIV
complex. The prototypical quinolone antibiotic
nalidixic acid was discovered in the early 1960s
and has since been replaced by compounds with
higher potency and improved dosing modalities
such as moxifloxicin and ciprofloxacin.
Resistance has emerged to the quinolone
antibiotics in Gram-positive and Gram-negative
strains. A summary of hospital surveys from 1997[(Figure_3)TD$FIG]
to 2001 showed an expanding rate of resistance
across infectious species [58]. Resistance
mechanisms include increasing drug efflux or
mutating the genes that code for DNA gyrase
and topoisomerase IV. Structural studies of a
DNA–topoIV cleavage complex with bound
moxifloxicin (Fig. 3) reveal the effects of amino
acid mutations in the quinolone-resistance-
determining region (QRDR), located in the GyrA
subunit [59]. Other drug-binding models
attempt to explain the effects of other resis-
tance-conferring mutations [60,61]. Compounds
that inhibit DNA cleavage via a new binding
mechanism that evades the fluoroquinolone
resistance mutations and compounds that
simultaneously inhibit GyrB/ParE ATPase func-
tion represent promising new approaches to
overcome resistance.
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[(Figure_4)TD$FIG]
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FIGURE 4
Crystal structure of GSK299423 bound to ParB [62].
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The topoIV/GyrA subunit inhibitor GSK299423
(Fig. 4) inhibits the turnover of the DNA cleaved
complex by stabilizing the enzyme–DNA complex
before cleavage and inhibiting separation of the
DNA strands. In this way, GSK299423 employs a
mechanism that is significantly different from that
of the fluoroquinolones [62]. The binding site for
GSK299423 is highly conserved in bacteria and
does not overlapwith the known binding sites for
fluoroquinolones, creating a potent inhibitor that
shows antibacterial activity against a range of
resistant strainswithmutations inDNAgyrase and
topoisomerase IV.
Using the topology of the binding sites of DNA
gyrase (GyrB) and topoisomerase IV (ParE),
(reviewed in Ref. [63]), novel classes of inhibitors
of the ATPase activity have been designed to
circumvent the resistance observed with qui-
nolones. Interestingly, these compounds also
overcome the resistance associated with the
coumarins and cyclothialidines [64,65] that bind
in a region that overlaps the ATP-binding site
[66,67]. These ATPase inhibitors inhibit gyrase
and topoisomerase IV simultaneously, thus
yielding an advantage in that the emergence of
resistance would require the unlikely occurrence
of simultaneous mutations. Combinations of
virtual screening and HTS led to compound A
(Fig. 1e), which was of modest potency. Com-
pound A was optimized using structure-based
design to arrive at B, a compound that displayed
nanomolar Ki values against S. aureus and
Escherichia coli gyrase and topoisomerase IV, and
impressive MIC90 values of 0.03–0.12 mg/ml
against a range of bacteria. This compound has
since spawned a wide variety of related che-
motypes from several other companies [65,68–
70], such as compound C, recently reported by
Pfizer [69].
Drug resistance in enzymes targeted by
antiviral agents
Most antiviral therapy is rightly focused on vac-
cine development. However, for a growing
number of viruses vaccines have remained elu-
sive, or the virus evolves so quickly that their
scope is limited. Although some successful anti-
viral agents target viral entry, several target the
viral enzymes that include: proteases, transcrip-
tases, integrases and neuraminidases. As with all
quickly evolving diseases there are challenges in
developing inhibitors that are robust; one strategy
is to target enzymes that are evolutionarily con-
strained. The viral proteases, which cleave several
diverse substrates, represent anexample of sucha
class and, to retain activity, the protease must
cleave all the substrates.
HIV protease inhibitors
HIV protease, which cleaves Gag and Gag-Pro-Pol
polyproteins at ten varied sites necessary for the
maturation of virus [71], is a major therapeutic
target for antiviral drugs. During the past 20
years, structure-based drug discovery efforts
have led to the development of nine approved
competitive active site protease inhibitors (PIs).
These inhibitors are the most potent anti-HIV
drugs and essential components of highly active
antiretroviral therapy (HAART) [72,73].
The development of drug resistance is a major
reason for the failure of PI therapy. The virus
accumulates many mutations within the pro-
tease that prevent PIs from binding to the pro-
tease. More than half the residues within the
protease mutate in different combinations and
lead to drug resistance [74,75]. Drug resistance is
a subtle change in the balance of recognition
events: the protease is still able to recognize and
process the natural substrate sites in the Gag and
Gag-Pro-Pol polyprotein, at the same time no
longer being effectively inhibited by the com-
petitive inhibitor. When resistance emerges the
interactions of the protease with an inhibitor are
significantly altered, whereas the interactions
with a natural substrate are maintained.
Crystallographic studies of the wild-type
protease bound to inhibitor molecules have
shown that most of the PIs occupy a similar
volume and contact similar residues within the
active site of the protease. Drug resistance
occurs where inhibitor atoms protrude beyond
the substrate envelope and contact protease
residues [76]. Thus, mutations at these sites
would specifically impact inhibitor binding while
maintaining substrate cleavage. The observation
that many of the drug-resistant mutations in the
active site do not contact the substrates has led
to the development of the substrate envelope
hypothesis: inhibitors that fit well within the
substrate envelope would be less susceptible to
drug resistance because a mutation that affects
inhibitor binding would simultaneously impact
the recognition and processing of themajority of
the substrates [76]. Of the currently prescribed
inhibitors the most potent is darunivar (DRV)
and, although not designed with the substrate
envelope constraint, DRV fits well within this
volume [2,77]. DRV in combination with ritinovir
has a high genetic barrier to resistance [78].
Developing robust HIV-1 PIs that avoid drug
resistance has proven to be a challenging task,
and the substrate envelope hypothesis provides
an approach to solving this problem. A survey of
five approved drugs using quantitativemeasures
of the bound inhibitor outside the substrate
envelope indicated that the exterior volume of
the inhibitors correlated with the loss of affinity
to mutant proteases [79]. The ability of the
substrate envelope to correlate with resistance
mutations prompted the prospective design of
new inhibitors with a lower likelihood of
developing resistance [3,80–83]. These studies
assist in validating the use of the substrate
envelope hypothesis [84] in structure-based
drug design of novel HIV PIs and have yielded
several leads for potential new drugs.
Hepatitis C NS/3A protease inhibitors
Drug resistance is also a major obstacle in the
treatment of hepatitis C virus (HCV). An esti-
mated 180 million people worldwide are
infected with HCV [85]. The essential HCV NS3/
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4A protease is an attractive therapeutic target
responsible for cleaving at least four sites along
the viral polyprotein. Many PIs are currently in
clinical trials; however, multidrug resistance is
widespread and arises very quickly. A recent
study [86] compares the cocrystal structures of
substrate structures with cocrystal structures of
inhibitor complexes and shows that, as in the
case of HIV-1 protease [77,79,81–83,87,88], pri-
mary drug resistance occurs in HCV NS3/4A
where the inhibitors protrude away from the
substrate envelope.
These findings suggest a general model for
using the substrate envelope approach to pre-
dict patterns of drug resistance in other quickly
evolving diseases. For drug resistance to occur,
mutations must selectively weaken enzyme
affinity for an inhibitor without significantly
altering its activity. Mutations occur outside the
substrate envelope to achieve this effect,
because these molecular changes can selectively
alter inhibitor binding without compromising
enzyme activity. Whenever the interaction of a
drug target with its biological substrates can be
structurally characterized, we predict that drugs
designed to fit within the substrate envelope will
be less susceptible to resistance. Structure-based
design strategies can incorporate this as an
added constraint to develop inhibitors that fit
within the substrate envelope. As a general
paradigm, design efforts incorporating the
substrate envelope approach can lead to the
development of more-robust inhibitors that are
less susceptible to resistance.
Concluding remarks
Drug resistance negatively impacts the lives of
millions of patients and costs our society billions
of dollars by limiting the longevity of many of our
most potent drugs. Drug resistance develops so
rapidly that new drugs quickly become less
effective, as witnessed by the evolution of
resistance to existing anticancer and antimicro-
bial agents (antibiotics, antivirals, antifungals
and antiprotozoals). A recent survey of European
intensive care doctors indicated that 50% have
treated at least one patient with a Gram-nega-
tive pathogen that was totally or almost totally
resistant to all antibiotics during the previous six
months’ [89].
Drug resistance research has been very much
a disease-specific endeavor, which has limited
intellectual progress and breakthroughs. How-
ever, as shown here, we have highlighted many
parallels among quickly evolving diseases, such
as cancer and infectious disease. No single
approach to develop drugs that are less prone to
resistance will work for every drug target. Rather,
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several approaches will be needed to success-
fully develop new drugs that will work on targets
where resistance is an issue. One such approach
that we have highlighted in this Feature is to
define targets that are resilient and to then
develop robust inhibitors for those targets.
Acknowledgements
The authors thank John D. Williams, PhD, and
Bing Li, PhD, of Microbiotix, for technical
assistance with this manuscript. National
Institute of Health supports the investigators as
follows: ACA – R01 AI073375, R01 GM067542;
MPP – R01 AI082577; CAS – R01 AI085051, P01
GM66524, R01 GM65347.
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Amy C. Anderson1,2
Michael P. Pollastri1,3
Celia A. Schiffer1,4,*
Norton P. Peet1,51Institute for Drug Resistance,University of Massachusetts Medical School,364 Plantation Street, Worcester,MA 01605-2324, USA2Department of Pharmaceutical Sciences,University of Connecticut, 69 N. Eagleville Road,Storrs, CT 06269, USA3Department of Chemistry & Chemical BiologyNortheastern University,417 Egan Research Center,360 Huntingdon Avenue, Boston,MA 02115, USA4Department of Biochemistry and MolecularPharmacology, University of MassachusettsMedical School, 364 Plantation Street, Worcester,MA 01605-2324, USA5Microbiotix, Inc., One Innovation Drive, Worcester,MA 01605-4306, USA
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