The Role of the acidity of N-heteroaryl sulfonamides as inhibitors of Bcl-2 family protein-protein interactions

Article abstract of DOI:10.1021/ml300321d

Overexpression of the antiapoptotic members of the Bcl-2 family of proteins is commonly associated with cancer cell survival and resistance to chemotherapeutics. Here, we describe the structure-based optimization of a series of N-heteroaryl sulfonamides t

Full text of DOI:10.1021/ml300321d

Letter
pubs.acs.org/acsmedchemlett
The Role of the Acidity of N‑Heteroaryl Sulfonamides as Inhibitors of
Bcl‑2 Family Protein−Protein Interactions
B. Barry Toure, Karen Miller-Moslin, Naeem Yusuff, Lawrence Perez, Michael Dore, Carol Joud,
́
́
Walter Michael, Lucian DiPietro, Simon van der Plas, Michael McEwan, Francois Lenoir, Madelene Hoe,
Rajesh Karki, Clayton Springer, John Sullivan, Kymberly Levine, Catherine Fiorilla, Xiaoling Xie,
Raviraj Kulathila, Kara Herlihy, Dale Porter, and Michael Visser*
Novartis Institutes for BioMedical Research Inc., 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
S
* Supporting Information
ABSTRACT: Overexpression of the antiapoptotic members of the Bcl-2 family
of proteins is commonly associated with cancer cell survival and resistance to
chemotherapeutics. Here, we describe the structure-based optimization of a series
of N-heteroaryl sulfonamides that demonstrate potent mechanism-based cell
death. The role of the acidic nature of the sulfonamide moiety as it relates to
potency, solubility, and clearance is examined. This has led to the discovery of
novel heterocyclic replacements for the acylsulfonamide core of ABT-737 and
ABT-263.
KEYWORDS: B cell lymphoma, Bcl-2 family, protein−protein interaction, apoptosis, cancer
poptosis, or programmed cell death, is the process by
which the maintenance of tissue homeostasis is controlled.
our interest in discovering novel Bcl-2 antagonists,11 we present
here our attempts to address these issues by replacing the acyl
sufonamide moiety of 1 with heterocyclic rings.12
A
Evasion of cell death is a hallmark of cancer progression and
development of resistance to chemotherapy.1 Bcl-2 family
proteins are key regulators of the mitochondrial apoptosis
pathway. The Bcl-2 family is comprised of both proapoptotic
(e.g., Bad, Bik, Bim, Bid, Noxa, and Puma) and antiapoptotic
(e.g., Bcl-2, Bcl-xL, Bcl-w, Mcl-1, and A1) proteins, which
regulate apoptosis through protein−protein interactions.2,3
Protein−protein interactions are central to many biological
processes and represent a large and important class of potential
therapeutic targets. Disruption of protein−protein interactions
with low molecular weight compounds remains a challenging
endeavor. This is due in part to the relatively large surface area
and lack of defined or specific pockets, which characterize most
protein−protein interfaces.4
In an effort to discover and develop Bcl-2 family antagonists,
Abbott scientists described a series of N-acyl sulfonamide-based
inhibitors such as ABT-737 (Table 1, entry 1).5−7 These
compounds demonstrate potent mechanism-based killing of
Bcl-2- and Bcl-xL-dependent cell lines by disrupting the
protein−protein interaction of prosurvival Bcl-2 proteins with
prodeath BH3-only proteins. One potential liability with this
series of inhibitors is its limited solubility, which leads to
dissolution-limited oral absorption.8 Central to this series of
inhibitors is an acylsulfonamide moiety, which acts as a linker
for two pocket binding moieties. This acylsulfonamide linker
presents a potential metabolic liability as exemplified by its use
as a prodrug of a primary sulfonamide.9,10 As a continuation of
An examination of the cocrystal structure of 1 and Bcl-xL
reveals the coplanarity of the aromatic ring and the carbonyl of
the acyl sulfonamide group.13 We rationalized that replacement
of the carbonyl with an unsaturated ring would maintain the
proper vectors for the two pocket binding moieties of the
molecule (see Table 1). In addition, introduction of bicyclic
ring systems with one saturated ring would decrease the
planarity of the core ring system and result in an increase in
aqueous solubility.14
Surface plasmon resonance (SPR) was used to characterize
each Bcl-2 inhibitor. An IC50 was determined through a
competition experiment with biotinylated Bak bound to the
surface and subsequent injection of a mixture of inhibitor and
Bcl-2 through the flowcell. For more potent compounds,
binding constants (KD) with Bcl-2 were determined by SPR to
allow compound differentiation.15 As shown in Table 1, initial
replacement of the acyl sulfonamide with a naphthyl ring (entry
2) led to a complete loss of binding affinity. While this result
was disappointing, as a confirmation of the design hypothesis,
we were encouraged by the quinoline 3, which showed an IC50
of 68 nM. This highlights the importance of the acidity of the
Received: October 5, 2012
Accepted: January 4, 2013
Published: January 4, 2013
© 2013 American Chemical Society
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ACS Medicinal Chemistry Letters
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Table 1. Activity of N-Heteroaryl Sulfonamides
a
b
Average of at least two measurements (duplicate IC50 or LD50 values were generated in each assay). Calculated pKa for compounds in table using
Moka.
sulfonamide NH. While the naphthyl NH has a predicted pKa
of 8, the quinoline NH is expected to be significantly more
acidic due to the combined inductive effect and the potential
for intramolecular H-bonding. This observation led to the
design of analogues, which would contain more acidic
sulfonamide moieties to more closely match the acidity of the
acyl sulfonamide moiety of ABT-737.
It was hypothesized that the synthesis of electron-with-
drawing heterocyclic cores would result in increased acidity of
the appended sulfonamide NH as compared to the naphthyl
analogue 2. The pyrazolo pyrimidine 4 was synthesized and
shown to have an IC50 of 8500 nM. Conversely, the triazole 5
had a potency of 25 nM and induced apoptosis in the Bcl-2-
dependent Toledo cell line with an LD50 of 4.8 μM. The
saccharin analogue 6 was a similarly potent Bcl-2 inhibitor with
an IC50 of 17 nM, although the compound had poor cell
activity. The lack of cell activity of 6 is rationalized by the poor
permeability demonstrated in in vitro assays (Table 3) perhaps
Figure 1. Crystal structure of 6 (blue) complexed with Bcl-2 at 2.1 Å
(4IEH) overlaid with the crystal structure of ABT-737, 1 (purple),
due to its high PSA (160).
complexed with Bcl-2.
Examination of the cocrystal structure of the saccharin
analogue with the Bcl-2 protein gave some insight into its
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ACS Medicinal Chemistry Letters
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Table 2. Activity of Saturated Ring Systems
a
Average of at least two measurements (duplicate IC50 or LD50 values were generated in each assay).
increase in binding affinity. As shown in Figure 1, compound 6
has a high degree of overlap with the binding mode of ABT-737
cocrystallized with Bcl-2. This highlights the importance of the
vector created by the saccharin core scaffold for the pocket-
binding moieties. In addition, 6 benefits from an electrostatic
interaction between Y67 and the oxygen of the sulfonyl group.
The difference in potency of entry 4 versus 5 and 6 could be a
result of the methyl substituent on the pyrazole ring of 4
interfering with the electrostatic interaction with Y67.
Compound 5 also shows a 4-fold increase in solubility over
compound 1. The solubility benefit of 5 is lost in compound 6
as the ionic character of the sulfonamide increases due its
increased acidity as a result of the electron-withdrawing
saccharin core.
Our focus then turned to ring systems with one saturated
ring to decrease the planarity of the core ring system in an
effort to increase solubility and permeability of our compounds
and thereby improve cellular potency. On the basis of the
crystal structure of 6, compounds were designed to maintain a
hydrogen bond acceptor in a suitable position to interact with
Y67. This led to the series shown in Table 2. The saturated six
member ring compound 7 had an IC50 of 317 nM. The
alternative six/five ring system 8, where the five member ring
was saturated, afforded a 2-fold loss in potency to 740 nM. The
five/seven ring system 9 was synthesized to vary the vector in
which the two pocket binding groups were and was found to
have an IC50 of 25 nM. However, this compound had a cell
potency of 3.47 μM. The six/six ring system 10 was found to
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ACS Medicinal Chemistry Letters
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a
Scheme 1. Synthesis of Piperdyl Pyrimidine 10
a
Conditions: (a) H2 Pd/C, Boc2O, DIPEA. (b) Formamidine, EtONa. (c) CCl4, PPh3, EtOH. (d) Pd2(dba)3, Cs2CO3, DavePhos, dioxane. (e) TFA,
DCM. (f) Na(OAc)3BH, THF. (g) Na(OAc)3BH, THF. (h) HCl, dioxane.
et al. delivered the desired product in excellent yield.16 Thus,
a
Table 3. In Vivo Pharmacokinetics in Sprague Dawley Rat
Pd-mediated coupling with the known aryl sulfonamide 138
parameters
10
6
19
89
forms 14. Removal of the Boc group and reductive amination
with ketone 15 (which is separately prepared from coupling of
the aldehyde 16 and piperdine 17) affords the final product 10.
While the cell potency of 10 was encouraging, the
pharmacokinetics in rat, as shown in Table 3, demonstrated
high clearance with little oral bioavailability. We attempted to
block potential metabolically labile positions to decrease
clearance. Substitution on the biphenyl ring system with
fluorine, 18, afforded a 2-fold increase in potency in both
binding and cell assays. Substitution at the benzylic position of
the biphenyl with a methyl, 19, gave a further increase in cell
potency to 0.113 μM. However, the clearance of compound 19
remained high, affording low exposure in plasma (Table 3). It
was observed that the clearance of compound 6 was
significantly reduced as compared to 10, affording a 4-fold
increase in AUC. Potentially, this reduction in clearance is
influenced by the greater acidity of the sulfonamide due to the
electron-withdrawing saccharin core of 6. Thus, in an attempt
to reduce the clearance of the series, analogues were designed
to increase the acidity of the sulfonamide by adding electron-
withdrawing groups to the piperidyl pyrimidine ring system.
This led to the synthesis of compounds 20, 21, and 22. The
piperidone analogue 20 had diminished binding and cell
potency. The Cl and CF3 substituted compounds 21 and 22
were potent binders of Bcl-2 with a KD of 17 and 10 nM,
respectively, although they had reduced potency in cell assays.
In summary, a series of Bcl-2 inhibitors with heterocyclic
cores has been prepared, which led to the discovery of potent
Cl (mL/min/kg)
Vdss (L/kg)
68
25
8.6
0.09
5.28
190
IV AUC (nmol/h)
PAMPA log Pe (cm2/s)
% F
232
−4.6
<5
761
<−6
<5
−4.8
ND
a
Plasma Cl and AUC calculated following 1 mg/kg iv dose. Oral
bioavailability (% F) calculated following a 10 mg/kg po dose. The
compound was administered as a solution in (a) 10% PG
(polyethylene glycol), 5% cremophor EL, and 85% pH citrate buffer
(10 and 6) and (b) 10% PG, 50 (10%) Solutol, and 40% WFI (water
for injection) (19).
have the best potency of the series with a Bcl-2 KD of 7 nM and
a cell potency of 0.298 μM. Compound 10 was also found to
inhibit Bcl-xL with an IC50 of 24 nM. Compounds 8, 9, and 10
demonstrated an increase in water solubility as compared to
compound 1.
With the improved cell potency of 10, we focused our efforts
on this six/six ring system. The synthesis of 10 is shown in
Scheme 1. Removal of the benzyl group of 11 and protection
with a Boc group affords the ketoester. Treatment of the
ketoester with formamidine forms the pyrimidine ring.
Chlorination of the pyrimidine ring proved problematic due
to incompatible reaction conditions with the needed BOC
protecting group; however, treatment with PPh3/CCl4 afforded
12. With 12 in hand, the stage was set for the challenging N-
heteroarylation of a complex sulfonamide. While copper-based
methods failed, a variant of the Pd coupling reported by Rivero
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ACS Medicinal Chemistry Letters
Letter
(14) Ishikawa, M.; Hashimoto, Y. Improvements in aqueous
solubility in small molecule drug discovery programs by disruption
of molecular planarity and symmetry. J. Med. Chem. 2001, 54, 1539−
1554.
(15) SPR provides a mass-based detection system that is automated,
enables parallel detection of interactions with peptide mimetics and
recombinant proteins, while also being free of the assay artifacts
encountered in fluorescence-based competition assays.
inhibitors with improved solubility over ABT-737. The acidic
nature of the sulfonamide NH has been shown to impact the
potency, solubility, and clearance rates of these compounds.
Potent cell active compounds have been discovered, and
strategies to modulate in vivo clearance rates have been
identified within the series. Further efforts to improve this
series are in progress and will be reported in due course.
(16) Burton, G.; Cao, P.; Li, G.; Rivero, R. Palladium-catalyzed
intermolecular coupling of aryl chlorides and sulfonamides under
microwave irradiation. Org. Lett. 2003, 23, 4373−4376.
ASSOCIATED CONTENT
■
S
* Supporting Information
Synthetic procedures and characterization data (1H NMR,
HRMS, and HPLC analysis) for selected compounds and
biochemical assay conditions. This material is available free of
charge via the Internet at http://pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
*Tel: 1-617-871-4294. E-mail: michael.visser@novartis.com.
■
Notes
The authors declare no competing financial interest.
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