Validating Eaton's Hypothesis: Cubane as a Benzene Bioisostere

Article abstract of DOI:10.1002/anie.201510675

Pharmaceutical and agrochemical discovery programs are under considerable pressure to meet increasing global demand and thus require constant innovation. Classical hydrocarbon scaffolds have long assisted in bringing new molecules to the market place, but an obvious omission is that of the Platonic solid cubane. Eaton, however, suggested that this molecule has the potential to act as a benzene bioisostere. Herein, we report the validation of Eaton's hypothesis with cubane derivatives of five molecules that are used clinically or as agrochemicals. Two cubane analogues showed increased bioactivity compared to their benzene counterparts whereas two further analogues displayed equal bioactivity, and the fifth one demonstrated only partial efficacy. Ramifications from this study are best realized by reflecting on the number of bioactive molecules that contain a benzene ring. Substitution with the cubane scaffold where possible could revitalize these systems, and thus expedite much needed lead candidate identification.

Full text of DOI:10.1002/anie.201510675

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International Edition: DOI: 10.1002/anie.201510675
German Edition: DOI: 10.1002/ange.201510675
Bioisosteres
Validating Eatonꢀs Hypothesis: Cubane as a Benzene Bioisostere
Benjamin A. Chalmers, Hui Xing, Sevan Houston, Charlotte Clark,
Sussan Ghassabian, Andy Kuo, Benjamin Cao, Andrea Reitsma, Cody-
Ellen P. Murray, Jeanette E. Stok, Glen M. Boyle, Carly J. Pierce, Stuart W. Littler,
David A. Winkler, Paul V. Bernhardt, Cielo Pasay, James J. De Voss, James McCarthy,
Peter G. Parsons, Gimme H. Walter, Maree T. Smith, Helen M. Cooper,
Susan K. Nilsson, John Tsanaktsidis,* G. Paul Savage,* and Craig M. Williams*
Dedicated to Professor Philip Eaton
on the occasion of his 80th birthday
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Abstract: Pharmaceutical and agrochemical discovery pro-
grams are under considerable pressure to meet increasing
global demand and thus require constant innovation. Classical
hydrocarbon scaffolds have long assisted in bringing new
molecules to the market place, but an obvious omission is that
of the Platonic solid cubane. Eaton, however, suggested that
this molecule has the potential to act as a benzene bioisostere.
Herein, we report the validation of Eatonꢀs hypothesis with
cubane derivatives of five molecules that are used clinically or
as agrochemicals. Two cubane analogues showed increased
bioactivity compared to their benzene counterparts whereas
two further analogues displayed equal bioactivity, and the fifth
one demonstrated only partial efficacy. Ramifications from this
study are best realized by reflecting on the number of bioactive
molecules that contain a benzene ring. Substitution with the
cubane scaffold where possible could revitalize these systems,
and thus expedite much needed lead candidate identification.
Figure 1. Two- and three-dimensional body diagonal views of cubane
(1) and benzene (2).
lack of interest in cubane presumably follows the incorrect
assumption that such compounds are esoteric, unstable, or
synthetically intractable.
Herein, we describe the first broad validation of Eatonꢀs
proposal that cubane (1) can act as a benzene (2) bioisostere.
An array of known biologically active molecules (3, 5, 7, 9,
and 11) with target indications ranging from cancer, Alz-
heimerꢀs disease, and pain to human parasites and agricultural
pests were chosen as diverse compounds to evaluate Eatonꢀs
benzene bioisostere hypothesis (4, 6, 8, 10, and 12; Figure 2).
The initial target selected for investigation was the histone
deacetylase inhibitor SAHA[8] (3, suberanilohydroxamic
acid), which gained approval from the FDA for the treatment
of cutaneous T-cell lymphoma (CTCL) in 2006.[9] The
comparative activities of SAHA (3) and its cubane analogue
(SUBACUBE 4) were determined by tumor cell (MM96L
and MCF7) and primary (NFF) line inhibition studies. When
incubated at various concentrations, both compounds inhib-
ited the growth of both tumor cell lines with similar IC50
values of 0.01 to 0.07 mgmLÀ1 when allowed to grow to
confluence (5–6 days). Both compounds were significantly
less toxic to NFF primary cells. Interestingly, SAHA (3)
exhibited a slightly greater toxicity towards NFF cells than 4.
In vitro analysis using the MyLa2059 cell line demonstrated
that both compounds were very efficient at killing the cell line
and significantly better than the vehicle (p < 0.001). The
in vivo tumor suppression activity of SUBACUBE (4) and
SAHA (3) was assessed in a T-cell lymphoma xenograft
model, which was generated by transplantation of MyLa2059
cells into NODSCIDIL2RgÀ/À (NSG) mice. Mice treated with
4 showed equivalent tumor growth rates relative to 3 (Fig-
T
he necessity for innovations to bolster pharmaceutical and
agrochemical discovery pipelines has become ever more
important to address current and future challenges in health
and food security.[1] Classical caged hydrocarbons, such as
norbornene and adamantane, have been widely used scaffolds
throughout the history of drug and agrochemical discovery
and still continue to deliver useful agents in the modern era.[2]
A hydrocarbon system missing from this scene, however, is
that of cubane (1, pentacyclo[4.2.0.02,5.03,8.04,7]octane),[3]
which Eaton predicted to provide fascinating potential for
pharmaceutical research.[4] This hypothesis was based on the
cubane framework being approximately the same size and
shape as a benzene ring (2) and thus a suitable bioisostere for
À
benzene replacement. Specifically, the C C bond length of
1.362 Š approaches that of benzene at 1.397 Š. Moreover, the
distance across the cube body diagonal (2.72 Š) is almost
equivalent to the distance across the benzene ring (2.79 Š;
Figure 1).[5]
Despite Eatonꢀs postulate in 1992, surprisingly few
cubane-containing molecules have been evaluated for phar-
maceutical/agrochemical potential[6] given the impact of
bioisosteres, for example, in drug discovery.[7] This apparent
[*] Dr. B. A. Chalmers, H. Xing, S. Houston, Dr. J. E. Stok,
Prof. P. V. Bernhardt, Prof. J. J. De Voss, Prof. C. M. Williams
School of Chemistry and Molecular Biosciences
University of Queensland (UQ)
C.-E. P. Murray, Prof. G. H. Walter
School of Biological Sciences, UQ (Australia)
Dr. G. M. Boyle, C. J. Pierce, Dr. C. Pasay, Prof. J. McCarthy,
Prof. P. G. Parsons
QIMR Berghofer Medical Research Institute
PO Royal Brisbane Hospital
Brisbane, 4072, Queensland (QLD) (Australia)
E-mail: c.williams3@uq.edu.au
Dr. C. Clark, Prof. H. M. Cooper
Brisbane, 4029, QLD (Australia)
Queensland Brain Institute, UQ (Australia)
Prof. D. A. Winkler
Dr. S. Ghassabian, Dr. A. Kuo, Prof. M. T. Smith
Centre for Integrated Preclinical Drug Development, UQ (Australia)
Monash Institute of Pharmaceutical Sciences
Parkville, 3052, MU (Australia)
B. Cao, A. Reitsma, S. W. Littler, Prof. D. A. Winkler,
Prof. S. K. Nilsson, Dr. J. Tsanaktsidis, Dr. G. P. Savage
CISRO Manufacturing, Ian Wark Laboratory
Melbourne, 3168, Victoria (VIC) (Australia)
E-mail: John.Tsanaktsidis@csiro.au
Prof. J. McCarthy
Australian Centre for International and Tropical Health
UQ (Australia)
Supporting information and ORCID(s) from the author(s) for this
article are available on the WWW under http://dx.doi.org/10.1002/
anie.201510675.
Paul.Savage@csiro.au
B. Cao, A. Reitsma, Prof. S. K. Nilsson
Australian Regenerative Medicine Institute, Monash University (MU)
Melbourne, 3168, VIC (Australia)
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There is an increasingly large demand for new pharma-
ceutical agents for the treatment of pain.[12] Thus the analgesic
effects of a widely used local anesthetic, the non-selective
sodium ion channel blocker benzocaine (7),[13] were directly
compared with cubocaine (8) and vehicle, following single
intraplantar bolus injections into one hind paw of adult male
Sprague–Dawley rats. An acute noxious heat stimulus was
applied to the ipsilateral (injected) hind paws immediately
pre-dose and at pre-defined intervals over a three hour post-
dosing period to generate paw thermal threshold (PTT)
versus time curves. The extent and duration of antinocicep-
tion evoked by 7, 8, and vehicle indicated that cubane
analogue 8 had the same local anesthetic efficacy as
benzocaine (7) in this model (Figure 3c).
The acaracide benzyl benzoate (9) is used as a topical
human treatment for scabies,[14] a very common skin disease in
developing countries that causes major morbidity. Although
highly effective, its use is limited by transient intense local
skin irritation.[15] All combinations of benzene ring replace-
ment were synthesized, giving three different cubane ana-
logues (10a–10c, Figure 2). When exposed to a solution of
benzyl benzoate (9; 25 mm), all scabies mites perished within
five minutes of exposure. A negative control assay consisting
of mites exposed to pure mineral oil showed no toxicity after
48 hours of exposure. When mites were exposed to 10a–10c,
Figure 2. Benzene-ring-containing pharmaceutical and agrochemical
compounds and the corresponding cubane analogues with hypothet-
ical trade names.
ure 3a). Both treatments were efficacious as
demonstrated by a significant reduction (p <
0.005) in tumor growth rate compared to the
vehicle-treated control mice. Thus cubane
analogue 4 performed almost identically to
SAHA (3).
In previous studies, administration of the
neotrophic drug leteprinim (5) was shown to
impart significantly increased neurite out-
growth, a measure of neuronal differentia-
tion, in PC12 neural precursor cells derived
from a rat pheochromocytoma.[10] Addi-
tional studies revealed neuroprotective
properties, which may provide a preventative
measure for stroke as well as other neuro-
degenerative diseases.[11] Treatment of PC12
cells with either leteprinim (5) or letepricube
(6) alone failed to induce neuronal differ-
entiation (Figure 3b). However, in combina-
tion with nerve growth factor (NGF), both
compounds induced neurite outgrowth when
compared to NGF alone. Moreover, in the
presence of NGF, the differentiation
capacity of cubane analogue 6 was markedly
greater than that of leteprinim (5). Despite
their ability to induce more vigorous neuro-
nal differentiation than NGF, 5 and 6 did not
enhance the length of neurites above that
induced by NGF alone (see the Supporting
Information), indicating that they influence
only the initial step in the neuronal differ-
entiation pathway.
Figure 3. Biological data for cubane analogues and their pharmaceutical and agrochemical
progenitors. a) Gompertz plot of tumor growth rates for animals treated with SUBACUBE
(4) and SAHA (3) versus control animals. Each line is a representative animal whose
tumor growth rate mirrors the average of mice in the relevant treatment group. b) NGF-
dependent PC12 cell differentiation was enhanced by letepricube (6). c) Extent and duration
of antinociception (DPTT AUC values) evoked by single intraplantar bolus doses of
benzocaine (7) or cubocaine (8). Negative control: water. d) Mean (ÆSE) mortality of
T. castaneum caused by different doses of diflucuburon (12; white) and diflubenzuron (11;
black). Different letters above the bars indicate significant differences (P<0.05) across
doses of particular test substances and across test substances.
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À
significantly lower activity was observed compared to the
with C H bond strength believed to be important in directing
positive control (9, 100% mortality). Cubyl cubate 10c
displayed the highest acaracidal activity at 55% mortality.
Furthermore, 10c required 24 hours to reach 55% mortality
compared to 5 minutes for benzyl benzoate.
oxidation. Thus, as cubane possesses unusually strong
À1
À
(BDE = 104 kcalmol ), but hindered tertiary C H bonds
because of the increased s character,[21] it is expected that
metabolism by hydroxylation of the cubane core would be
decreased. P450-catalyzed oxidation of a phenyl ring pro-
ceeds by addition to the electron-rich p-moiety and does not
Tribolium castaneum (rust-red flour beetle), is a major
pest of stored grain and derivative products worldwide and
has been tested with benzoyl phenyl ureas (BPUs), such as
diflubenzuron (11). This insect growth regulator is considered
most effective on the larval stages of the arthropods.[16] Late
instar larvae of laboratory-cultured T. castaneum were
exposed to diflubenzuron (11) and diflucuburon (12). The
latter (12) consistently and significantly outperformed the
former (11) in this (Figure 3d) and additional evaluations (see
the Supporting Information).
Of the five cases evaluated above, either in vitro or
in vivo, four cubane analogues were observed to manifest
equal (SUBACUBE 4, cubocaine 8) or increased bioactivity
(letepricube 6 and diflucuburon 12) compared to their
corresponding benzene counterparts. The cubyl cubates
(10a–10c), on the other hand, demonstrated only partial
efficacy.
occur by simple C H abstraction.[22] Nevertheless, it has been
À
suggested that hydroxylation of methylcubane occurs on both
the methyl moiety and the cubane core, although the latter
leads to decomposition of the cubane core.[23] With this in
mind, we evaluated the oxidation of tert-butylcubane (see the
Supporting Information) with a model bacterial P450 enzyme
(P450cam), which afforded only one detectable product,
apparently from hydroxylation at one of the methyl groups.
Interestingly, P450cam-catalyzed oxidation of analogous tert-
butylbenzene proceeded to give approximately equal
amounts of the products of aromatic ring and methyl
hydroxylation. These observations help to explain why the
diflubenzuron analogue (12) demonstrates such remarkable
activity. Diflubenzuron (11) has two known modes of
degradation, which promote resistance in arthropods:
1) acyl imide bond cleavage and 2) metabolic hydroxylation
of the aniline ring followed by conjugation to sugars and
excretion;[24] presumably, at least the latter pathway is
significantly diminished by cubane incorporation. Finally, to
determine whether cubane-for-benzene replacement would
promote alternative drug metabolism pathways, a phase I and
II metabolic analysis of both leteprinim (5) and its cubane
analogue (6) was undertaken. Utilizing in vitro human liver
microsomes, glucuronide metabolites were not observed for
either compound, indicating that neither of these compounds
was metabolized, and thus cleared, by this pathway.
Although cubane (1) itself is thermodynamically unstable
(DHf = 144 kcalmolÀ1) and highly strained (SE = 161.5 kcal
molÀ1), it and many of its known derivatives are indefinitely
stable at ambient temperatures. This anomaly arises because
cubane has no kinetically viable pathways for thermal
rearrangement: Carbon–carbon bond homolysis leads to
a high-energy biradical that is still very strained, and two-
bond ring-opening reactions are thermally disallowed by
orbital symmetry considerations.[25]
Perhaps the primary concern regarding the use of cubane
in both academic and industrial settings is the availability of
suitable cubane precursors on significant scale. This has
largely been addressed with our finding that dimethyl cubane-
1,4-dicarboxylate (13) can be produced in kilogram quanti-
ties.[26] All analogues (4, 6, 8, 10a–10c,[27] 12) were synthesized
from this precursor using standard transformations. A secon-
dary concern, however, is functional-group placement and
manipulation. When compared to synthetic chemistry asso-
ciated with the benzene ring, cubane chemistry is not as well
established. Nevertheless, the cubane core has proven to be
robust and is tolerant to a wide range of conditions [e.g., acid-
catalyzed transesterification (8) and deprotection (17), base-
mediated hydrolysis (14), Curtius rearrangement (8, 17, 20),
Barton decarboxylation (16) and chlorination (21) via the N-
hydroxy-2-thiopyridone (15), diazotization (12), and borane
reduction (19)], and for the most part, these transformations
What are the main implications for using the cubane motif
as a benzene bioisostere in future bioactive molecule discov-
ery in terms of solubility, metabolism, stability, and tract-
ability?
Solubility[17] and permeability are key parameters for
biomolecule design and discovery. SUBACUBE (4) had only
a slightly higher logP value (1.52) than SAHA (0.99). For
cancer cell line investigations, this had little impact, whereas
for the mouse studies, slight changes to the vehicle delivery
method were required to facilitate solubility. Letepricube (6)
did not require any changes in the testing regime because of
solubility issues, as was the case for the benzocaine analogue
(8, D(logP) = 0.07). However, it is surmised that the slight
increase in activity observed for 6 may be a reflection of
increased lipophilicity matching the known CNS hydrophobic
environment associated with myelination of nerve fibers.[18]
Diflucuburon (12) showed a logP difference of 0.2, which was
inconsequential for the T. castanuem study, because solid 12
was readily ingested by the target larvae. However, the cubyl
cubates (10a–10c) highlight the intrinsic differences in polar-
ity and subsequent effects on activity in some cases, when
considering substitution of a benzene ring moiety for the
cubane framework. In this extreme case, the delivery vehicle
(mineral oil) required heating to solubilize analogues 10a
(logP = 5.43) and 10b (logP = 5.10), but not for 10c (logP =
4.22; benzyl benzoate: logP = 3.86). Among the cubyl
cubates, 10c had the highest activity, albeit only 55%
compared to benzyl benzoate. These observations suggest
that it is important for cubane isostere design to aim for
solubility matching, except in such cases where cubane has
limited substitution to significantly alter the overall solubility
(i.e., cubyl cubates 10a–10c).
Phase I drug metabolism[19] is mainly carried out by
members of the cytochrome P450 superfamily and typically
À
results in insertion of an oxygen atom into a C H bond to
produce an alcohol.[20] The selectivity of this process is
determined by a combination of steric and electronic factors,
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Scheme 1. Synthesis of the cubane analogues 4, 6, 8, and 12. DMAP=N,N-dimethylaminopyridine, DMF=N,N-dimethylformamide, DPPA=di-
phenylphosphoryl azide, TEA=triethylamine.
gave similarly good yields to those obtained for the benzene
analogues (see Scheme 1 and the Supporting Information). In
both a synthetic and medicinal chemistry sense, recent work
has further demonstrated the synthetic potential of cubane
towards potentially biologically active pharmacophores.[28]
In summary, cubane can act as a suitable isostere for
benzene in biological applications, as postulated by Eaton,
with the caveat that biological uptake of the compound must
be feasible. This finding 1) provides a tangential chemical
bioisostere approach for drug and agrochemical discovery
and 2) will revitalize new and old commercial compounds that
have already been refined based on various drug discovery
principles, thus expediting lead candidate identification for
rapid pipeline bolstering.
tests. The Australian Regenerative Medicine Institute is
supported by grants from the State Government of Victoria
and the Australian Government.
Keywords: agrochemicals · bioisosteres · cubane ·
pharmaceuticals · structure–activity relationships
How to cite: Angew. Chem. Int. Ed. 2016, 55, 3580–3585
Angew. Chem. 2016, 128, 3644–3649
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Acknowledgements
This work was supported by the Australian Research Council
(Future Fellowship to C.M.W., FT110100851), the University
of Queensland, the CSIRO (Melbourne), NCRIS 2013 THD
grant funding to the TIA-QLD Node from Therapeutic
Innovation Australia (TIA), and infrastructure purchased
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Received: November 17, 2015
Revised: January 3, 2016
Published online: February 5, 2016
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