Exploring physicochemical space: Via a bioisostere of the trifluoromethyl and ethyl groups (BITE): Attenuating lipophilicity in fluorinated analogues of Gilenya for multiple sclerosis

Article abstract of DOI:10.1039/c8cc05643a

The direct, catalytic vicinal difluorination of terminal alkenes via an I(i)/I(iii) manifold was exploited to install a chiral, hybrid bioisostere of the CF₃ and Et groups (BITE) in Gilenya; the first orally available drug for the clinical management of Multiple Sclerosis (MS). This subtle fluorination pattern allows lipophilicity (logD) to be tempered compared to the corresponding CF₃ and Et derivatives (CH₂CH₃ > CH₂CF₃ > CHFCH₂F).

Full text of DOI:10.1039/c8cc05643a

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Marilyn M. Olmstead, Alan L. Balch, Josep M. Poblet, Luis Echegoyenet al.
Reactivity differences of Sc3N@C2n (2n 68 and 80). Synthesis of the
first methanofullerene derivatives of Sc N@D5h-C80
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Exploring Physicochemical Space via a Bioisostere of the
Trifluoromethyl and Ethyl Groups (BITE): Attenuating Lipophilicity
in Fluorinated Analogues of Gilenya® for Multiple Sclerosis
Received 00th January 20xx,
Accepted 00th January 20xx
Nathalie Erdeljac,a Gerald Kehr,a Marie Ahlqvist,b Laurent Knerr*c and Ryan Gilmour*a,d
DOI: 10.1039/x0xx00000x
www.rsc.org/
in a manner antipodal to classic steric approaches. These subtle
changes in fluorination pattern can also be harnessed to fine-tune
The direct, catalytic vicinal difluorination of terminal alkenes via
an I(I)/I(III) manifold was exploited to install a chiral, hybrid
bioisostere of the CF3 and Et groups (BITE) in Gilenya®; the first the physicochemical profiles of small molecule drug candidates:
This has been elegantly demonstrated by Müller and Carreira.4
orally available drug for the clinical management of Multiple
Sclerosis (MS). This subtle fluorination pattern allows lipophilicity
(log D) to be tempered compared to the corresponding CF3 and Et
derivatives (CH2CH3>CH2CF3>CHFCH2F).
Inspired by the structure-function interplay of fluorination
patterns in medicinal chemistry, and in response to a deficiency in
the synthesis repertoire, we recently reported a direct, catalytic,
vicinal difluorination of terminal alkenes.5 Catalysis proceeds via an
I(I)/I(III) manifold that exploits Selectfluor® as the terminal oxidant,
whilst HF•amine serves as both an inexpensive fluoride source and
Brønsted acid. Since the resulting vicinal difluoro-motif is a chiral,
hybrid bioisostere of the trifluoromethyl and ethyl groups (BITE
Structural editing with fluorine is a ubiquitous strategy to modulate
the physicochemical and pharmacological properties of small
molecule drug candidates. Parameters ranging from lipophilicity,
intrinsic potency, metabolic stability through to the pKa of proximal
functional groups underscore the strategic value of fluorination in
contemporary medicinal chemistry.1 Often, the electronic factors
that govern these physicochemical characteristics manifest
themselves in molecular topology and can thus be rationalised at
the structural level. This is particularly pronounced in acyclic
systems when fluorine is situated vicinal to an electron deficient
motif (X = F, O, N, S).2,3 In such scenarios, the synergistic interplay of
group),2e,6
a suitable platform was sought to explore the
physicochemical profile of this unit (Figure 1). Specifically,
lipophilicity was of interest due to its importance in the early stages
of drug development and associated requirement to generate
molecular “fragments” to tailor the overall quality and “drug-
likeness” of a candidate.7
-
stereoelectronic (σC-H→σC-F*) and electrostatic (R+…Fδ ) interactions
Bioisostere concept
ensures that syn-clinal conformers are significantly populated (the
Gauche Effect). Predicated on a donor acceptor model, F-C-C-(X)
dihedral angles approaching 60° ensure maximum orbital overlap
and also allow the fluorine atom to engage in stabilising Coulombic
interactions with proximal cations. Consequently, judicious aliphatic
fluorination provides an expansive platform to steer conformation
F
F
F
*
F
CH3
F
Bioisostere
Direct vicinal
difluorination
and
BITE
Et
CF3
Fig.
1 The BITE group: A chiral, hybrid bioisostere of the
trifluoromethyl and ethyl groups.
Lipinski highlighted the significance of this parameter in his “rule of
five”, to lower attrition rates during drug discovery, which suggests
that the desired clogP for orally administered drugs should not
exceed 5.8 While the influence of fluorine substitution on aryl ring
systems generally leads to a moderate increase in lipophilicity, the
effects on aliphatic systems are more complex.4,9 To that end, we
sought to explore the effect of the BITE group on the lipophilicity of
fluorinated analogues of the multiple sclerosis drug Fingolimod /
Gilenya® (Figure 2).
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In addition, the synthesis of the non-fluorinated (Et) and
trifluoromethylated (CF3) counterparts was performed to allow for
a comparative physicochemical profiling of the three substituents
(Figure 3: Target scaffolds).
Fig. 2 The natural product Myriocin and the relapsing-remitting
multiple sclerosis drug Fingolimod / Gilenya®.
Multiple sclerosis (MS) is a chronic inflammatory disease of the
central nervous system (CNS) in which demyelination and axon
damage leads to the dysfunction and death of neural cells.10 With a
usual age of onset around 30 years, MS is considered to be the
most prevailing cause of disability among young adults and is
estimated to affect around 2.1 million people worldwide.11 So far,
there is no cure for MS and current treatment strategies rely on
various disease modifying drugs (DMO) to reduce relapse rates and
slow down the progression of the disease.12 First-line therapy
continues to consist of intramuscular (IM) or subcutaneous (SC)
administration of interferon betas (Avonex®, Biogen Idec;
Betaferon®, Bayer; Extavia®, Novartis Pharma) or glatiramer acetate
(Copaxone®, Teva Pharmaceutical Industries).13 In 2010, Fingolimod
(Gilenya®, Novartis Pharma) was approved by the US Food and Drug
Administration (FDA) as the first orally bioavailable drug for the
treatment of relapsing-remitting multiple sclerosis (RRMS).14 As a
structural analogue of the naturally occurring sphingosine myriocin
(Figure 2), fingolimod is phosphorylated in vivo by sphingosine
kinase 2 to its active metabolite S-fingolimod-phosphate.15 Its
immunomodulatory effects are mediated via initial activation of
sphingosine 1-phosphate (S1P) receptors on lymphocytes, which
obstructs their egress from the lymph nodes into the peripheral
circulation and thereby reducing their infiltration into the CNS.16
As a platform to validate the BITE group as a physicochemical
handle to modulate lipophilicity in small molecule drug candidates,
fluorinated analogues of Fingolimod (Gilenya®) were investigated.
The direct, catalytic difluorination of terminal alkenes5 accelerated
this investigation by allowing hydrocarbon tails with 1,2-
difluorinated alkyl chains of varying length to be rapidly prepared.
Scheme 1 Synthesis of the aromatic core. Reagents and conditions
[yield]: (a) BnBr, K2CO3, DMF, r.t. [99%]; (b) H3CPPh3I, NaH, THF, r.t.
[96%]; (c) (i) BH3/THF, 0 °C to r.t. and (ii) NaOH, H2O2, EtOH/H2O, 0
°C to r.t. [82%]; (d) I2, PPh3, imidazole, CH2Cl2, 0 °C to r.t. [99%]; (e)
NaH, AcNH(COOEt)2, DMF, 95 °C [63%]; (f) (i) LiCl, NaBH4, THF/EtOH,
0 °C to r.t. and (ii) Ac2O, Et3N, DMAP, THF, r.t. [75%]; (g) H2, Pd/C,
EtOH, r.t. [92%].
Synthesis: The small library of compounds was prepared from a
common precursor 8 in a highly concise manner (Scheme 1).
Commercially available p-hydroxy benzaldehyde 1 was processed to
the corresponding styrene 3 via a benzylation / methylenation
sequence. Subsequent hydroboration / oxidation furnished alcohol
4, which was converted to the iodide 5. The drug head group was
installed by displacement using diethyl acetamidomalonate to
furnish 6 prior to double reduction of the esters and acetate
protection (7). Finally, debenzylation liberated phenol 8 as a handle
to install the alkyl spacer for physicochemical modulation.
Table 1 Catalytic, vicinal difluorination of alkenes via an I(I)/I(III)
manifold.
10
X
n
Yield [%]
a
b
c
d
e
f
OTs
OTs
OTs
OTs
OTs
Br
1
2
3
4
5
6
48
46
72
79
55
72
The alkyl chains containing the vicinal BITE motif required for
coupling with 8 were prepared directly from the corresponding
terminal alkenes (Table 1, 9a-f → 10a-f). To that end, p-iodotoluene
was employed as a catalyst to generate the requisite p-TolIF2
species in situ. This was enabled by utilizing Selectfluor® as oxidant,
Fig. 3 The Gilenya® analogues for comparative physicochemical
profiling.
2 | J. Name., 2012, 00, 1-3
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and a mixture of Olah’s reagent and Et3N•5HF as both the HF Fig. 4 Measured logD7.4 profile of the compounds in the different
source and Brønsted acid activator (Table 1).5 The desired 1,2- series as a function of the methylene spacer length: alkyl (grey),
difluorinated products were obtained in racemic mixture in trifluoromethyl (green), 1,2-difluoroethyl (blue). Fingolimod has
moderate to good yields (up to 79%). The corresponding been added as reference (red). The labels indicate the individual
trifluoromethylated and non-fluorinated hydrocarbon chains were measured logD7,4 values. For a detailed description of the assay see
either obtained commercially or prepared from available starting the supporting information.
materials (full details are provided in the Supporting Information).
Finally, the aliphatic chains were coupled to the Gilenya® head
4
3.5
3
4
3.5
3
group 8 via displacement chemistry (11a-f, 13a-e and 15a-f, BITE
group, CF3 and Et, respectively) and the target molecules were
globally deprotected and converted to their respective
hydrochloride salts (Scheme 2, 12a-f, 14a-e and 15a-f, BITE group,
CF3 and Et respectively). For the comparative physicochemical
analysis, the parent drug Gilenya® was also synthesised as a
reference (full details are provided in the Supporting Information).17
Difluoro
Trifluoro
Alkyl
3.2
2.5
2.7
2.5
2
Gilenya®
1.9
2.1
0.7
1.9
1.4
1.6
1.5
1
1.3
0.8
1.1
0.5
0
0.5
-0.2
1
0.2
-0.5
0
2
3
4
5
6
Methylene spacer (n)
Table 2 Lipophilicity, solubility, apparent passive permeability and
in vitro metabolic stability comparison of compounds described.a
See supporting information for assay details.b All compounds were
stable in the presence of human microsomes (Clint (µM/min/mg)
<4.5).
Rat/Human
Caco-2
Solubility
(pH7.4,
µM)a
Hepatocytes
Clint
Papp
(10-6
a
Scheme 2 Coupling of the aliphatic chains to 8, deprotection and
hydrochloride salt formation. Reagents and conditions [yield]: (a)
K2CO3, DMF, r.t. [11a-f 36-94%, 13a-e 66-88%, 15a-f 72-97%]; (b) (i)
aq. LiOH (2M), MeOH, reflux and (ii) HCl in dioxane (4M), r.t. [12a-f
39-90%, 14a-e 48-73%, 16a-f 47-99%].
Entry
n
LogD7.4
(μL/min/10-
6 cells)a,b
cm/s)a
Fingolimod
12a
5
1
2
3
4
5
6
2
3.5
-0.2
0.2
0.5
0.7
1.3
2
-
12.8/-
1.53/-
2.67/-
9.91/<1
10.6/-
20.3/-
968
875
874
585
133
-
1.19
0.84
-
12b
12c
12d
12e
Physicochemical Profiling: Compounds 12a-f, 14a-e and 16a-f were
subjected to in vitro profiling to assess the impact of BITE
fluorination on lipophilicity, solubility, passive permeability and
metabolic stability (Table 2). Predictably, the introduction of the
trifluoromethyl (CF3) group had a clear effect on lipophilicity
compared to the alkyl series (average ꢀlogD7.4 = -0.4) (Figure 4). As
expected, and in line with previously published data,4 the effect of
vicinal difluoroethyl BITE group was significantly more pronounced
(average ꢀlogD7.4 = -1.5 and -1.2 versus the alkyl and trifluoromethyl
series, respectively). Furthermore, the vicinal difluoroethyl BITE
series performed better in terms of solubility compared to the
roughly comparable trifluoromethyl and alkyl series: This was
especially apparent for larger alkyl groups (5 to 10 fold better
solubility for n=3 and above) (Figure S1). It is interesting to note
that, despite an average lower lipophilicity, the trifluoromethyl
series performed poorer in that regard compared to the alkyl series.
As expected, the passive permeability measured using a Caco-2
assay (Figure S2) showed a clear relationship with the lipophilicity
(Table 2).
-
12f
14a
14b
14c
14d
14e
16a
16b
16c
16d
16e
16f
1.9
1.1
1.6
2.1
2.7
3.2
0.8
1.4
1.9
2.5
3
59
152
88
65.1
16
5.8
1000
796
175
58
-
47.3/-
8.28/-
11.6/<1
15.8/-
37.3/-
12.3/-
15.9/-
11.9/-
12.3/3.34
9.90/-
13.1/-
11.5/-
2.61
2.95
-
-
-
-
5.09
5.02
-
-
-
3
4
5
6
1
2
3
4
5
6
5
4
4
Indeed, the more polar vicinal difluoroethyl BITE derivatives studied
demonstrated low permeability compared to their trifluoromethyl
analogues. This was even more pronounced in comparison to the
alkyl systems, which showed moderate to high permeability (Table
2). The metabolic stability measured in rat and human hepatocytes
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(see Supporting Information for assay details) revealed a clear
correlation between Rat Clint (unbound) versus logD and
demonstrated a positive impact of fluorine introduction in that
respect (Figure S3). There is, however, a disconnect between Clint
in human and rat hepatocytes (12c and 14b), which could be due to
differences in metabolism in these two species. All compounds
reported here were however stable in the presence of human liver
microsomes (Clint (µM/min/mg) <4.5).
J. Chem., 2017, 57, 92-100; (h) M. Aufiero, R. Gilmour, Acc.
Chem. Res., 2018, 51, 1701-1710.
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Gilmour, Chem. Sci., 2015, 6, 3565-3571; (b) C. Thiehoff, L.
Schifferer, C. G. Daniliuc, N. Santschi, R. Gilmour, J. Fluorine
Chem., 2016, 182, 121-126; (c) N. Santschi, C. Thiehoff, M. C.
Holland, C. G. Daniliuc, K. N. Houk and R. Gilmour,
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Conclusions
Contemporary medicinal chemistry requires new areas of
chemical space to be explored to place physicochemical
parameters on a structural foundation. The hybrid bioisostere
of the CF3 and Et groups (BITE group) has been found to
attenuate lipophilicity in a series of fluorinated analogues of
the Multiple Sclerosis drug Gilenya®. Comparative
physicochemical profiling with the corresponding CF3 and Et
derivatives demonstrated that lipophilicity (log D) can be
tempered in the order CH2CH3>CH2CF3>CHFCH2F. In addition, a
comparison of the three groups on solubility, apparent passive
permeability and in vitro metabolic stability has been
established. Efficient installation of the BITE group was
achieved by direct, catalytic vicinal difluorination of α-olefins
without the need for substrate pre-functionalisation.
5
6
7
8
9
C. A. Lipinski, F. Lombardo, B. W. Dominy, P. J. Feeney, Adv.
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We gratefully acknowledge generous financial support
from the WWU Münster, the DFG (“Cells in Motion, Cluster of
Excellence” CiM, and SFB 858), and the European Research
Council (ERC-2013-StG Starter Grant 336376-ChMiFluorS to
RG).
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Conflicts of interest
There are no conflicts of interest to declare.
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