A structure-Permeability study of small drug-like molecules

Article abstract of DOI:10.1016/S0960-894X(02)01035-1

A systematic structure-permeability relationship study on a set of small drug-like molecules with log D values in the range -2.5 to 3 and carrying a diverse array of functionality reveals that the compounds with log D>0 and <3 are highly permeable. Surprisingly, several tetrazole derivatives were found to be substrates for efflux pump(s).

Full text of DOI:10.1016/S0960-894X(02)01035-1

Bioorganic & Medicinal Chemistry Letters 13 (2003) 719–722
A Structure–Permeability Study of Small Drug-like Molecules
Thomas Fichert,a Mehran Yazdanianb and John R. Proudfoota,*
aDepartment of Medicinal Chemistry, Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, PO Box368,
Ridgefield, CT 06877, USA
bDepartment of Pharmaceutics, Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, PO Box368,
Ridgefield, CT 06877, USA
Received 23 July 2002; accepted 1 November 2002
Abstract—A systematic structure–permeability relationship study on a set of small drug-like molecules with log D values in the
range ꢀ2.5 to 3 and carrying a diverse array of functionality reveals that the compounds with log D>0and <3 are highly
permeable. Surprisingly, several tetrazole derivatives were found to be substrates for efflux pump(s).
# 2003 Elsevier Science Ltd. All rights reserved.
The Caco-2 cell model is widely used as an indicator of
oral drug absorption1 and permeability data generated
in this assay has been published for various sets of
structurally diverse compounds and drugs.2 We have
previously used the Caco-2 cell model to evaluate the
cell permeability of peptidomimetic carboxylic acid
derivatives designed as ligands for the p56lck SH2
domain,3 and found that the data was useful in guiding
medicinal chemistry efforts to design molecules active in
cellular assays. Based on this experience we were inter-
ested in applying the model to a broader exploration of
structure–permeability relationships, particularly the
effect on cell permeability of some polar groups com-
monly used in lead optimization efforts. The introduc-
tion of such groups is sometimes necessary to improve
the molecular potency or physicochemical properties of
lead molecules but the effect on cellular activity can be
inconsistent. The few published4 systematic studies of
structure–permeability relationships have generally been
restricted in scope either because of a limited number of
compounds studied or a focus on peptide-like struc-
tures. Here, we present a systematic exploration of the
effect on cell permeability of some commonly used
functional groups attached to the drug-like5 core struc-
tures shown in Scheme 1.
from the appropriately substituted benzyl bromide by
N-alkylation of imidazole, benzimidazole or pyrazole,
respectively. For the synthesis of 14 and 15 the benzyl
bromides substituted with a sulfonic acid or sulfona-
mide group were obtained from the sulfonyl chloride by
hydrolysis or by treatment with ammonia.7 Pyrimidines
20, 21 and 22, were obtained by reaction of 2-chloro-
pyrimidine with activated zinc followed by nickel cata-
lyzed coupling8,9 with the appropriate benzyl bromide.
Carboxylic acids 23–27 were obtained by hydrolysis of
the corresponding methyl esters, while, alternatively,
treatment of the esters with ammonia gave amides 28–
31. Reduction of nitriles 8, 16, or 20 with hydrogen/
Raney–Ni gave the amines 32–34. The amidine 35 was
prepared from nitrile 20 by the Pinner reaction.10 The
tetrazoles 36–39 were formed from the corresponding
nitriles by treatment with sodium azide and ammonium
chloride.11 The methyl sulfonamide 41 was prepared by
stannous chloride reduction of nitro derivative 13 in
DMF12 followed by reaction of the aniline 40 with
methanesulfonyl chloride.
We evaluated compound permeability13 in the Caco-2
model following a standard protocol2a and the data is
presented in Table 1. Figure 1 illustrates graphically the
permeability data presented in Table 1. Compounds are
arranged according to the substituent attached to the
different core structures, and are categorized as having
high, moderate, or low permeability based on their per-
meability coefficients. For compounds displaying low
apical to basolateral (PA!B) permeability we also mea-
sured permeability in the basolateral to apical direction
The compounds6 evaluated in this study were prepared
as shown in Scheme 1. Compounds 1–19 were derived
*Corresponding author. Fax: +1-203-791-6072; e-mail: jproudfo@
rdg.boehringer-ingelheim.com
0960-894X/03/$ - see front matter # 2003 Elsevier Science Ltd. All rights reserved.
doi:10.1016/S0960-894X(02)01035-1

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T. Fichert et al. / Bioorg. Med. Chem. Lett. 13 (2003) 719–722
(PB!A) in order to determine whether active transport
was occurring. Such compounds were the benzoic
acids 4, 23, 24, the amidine 35 and the tetrazoles 36–39.
For these compounds, the PDR14 (permeability
directional ratio=PB!A/PA!B) is also shown in Table 1
along with Pt [estimated transcellular permeability=
(PA!B+PB!A)/2)].15
mide derivatives (15). Only for the imidazole carbox-
amide 28, which falls in the group of moderately
permeable compounds, does the nature of the hetero-
cycle influence permeability substantially. This com-
pound has decreased permeability compared to the other
carboxamide derivatives. The greater basicity of the imi-
dazole ring compared to the other heterocycles16 may
partially explain this result, but this alone is not sufficient
since the benzylamine derivatives 32–34 are highly
permeable while protonated to greater extent at pH 7.4.
Highly permeable compounds (permeability coefficient
>10ꢁ10ꢀ6 cm/s). This group, contains the core struc-
tures (1 and 6), nitriles (2, 8, 16 and 20), carboxamides
(29, 30 and 31), and aminomethyl (32, 33 and 34),
amino (40), methanesulfonylamido (41) and sulfona-
Moderately permeable compounds (permeability coeffi-
cient between 0.3ꢁ10ꢀ6 and 10ꢁ10ꢀ6 cm/s). All the car-
boxylic acid derivatives fall into this group. The charged
nature of these compounds at pH 7.4 is most likely
responsible for the moderate permeability. Within each
series, the imidazoles (4, 5 and 23) are consistently less
permeable than the other heterocycles. There is no sub-
stantial difference in permeability for the different car-
boxylic acids with the same scaffold. We also
determined B to A permeability for 4, 23 and 24, three
of the less permeable carboxylic acids and, while the
PDR value for compound 4 is 1, values of 2 and 3 for 23
and 24 indicate that these compounds can be moderate
substrates for cellular efflux pumps.
Poorly permeable compounds (permeability coefficients
<0.3ꢁ10ꢀ6 cm/s). This group contains the amidine 35,
tetrazoles 36–39 and sulfonic acid 14. Permeability
coefficients are in the range of the low permeable mar-
ker mannitol (0.17ꢁ10ꢀ6 cm/s). Since the amidine 35
and the sulfonic acid 14 are completely ionized at pH
7.4, low permeability was expected for these two com-
pounds. We were surprised, however, by the low per-
meability of the tetrazole derivatives 36–39 when
compared with the corresponding carboxylic acids.
The tetrazole group is frequently used as a carboxylic
acid replacement in medicinal chemistry,17 and we had
expected similar permeability properties for the tetra-
zoles and their carboxylic acid analogues. Since there
are no reports describing such a significant detrimental
impact of the tetrazole group on cell permeability, we
thought it prudent to determine whether the low A to B
permeability for these compounds could be due to
interactions with cellular efflux pumps. The PDR values
in Table 1 (20for tetrazole 39 and even higher values of
129, 145 and 180for tetrazoles 38, 37 and 36) indicate
that these compounds are substrates for efflux pumps.
The substrate specificity of efflux pumps is relatively
unexplored18 but these particular tetrazoles are appar-
ently recognized and actively transported. The amidine
derivative 35 and the least permeable compound in this
study, the sulfonic acid compound 14, are also moderate
substrates for efflux pumps as indicated by PDR values
of 3 and 7, respectively. The Pt values for tetrazoles 36
and 37 indicate that these compounds have high intrin-
sic cell permeability while tetrazoles 38 and 39 are
moderately permeable. Even the amidine 35 and sul-
fonic acid 14 fall in the category of moderately perme-
able compounds when evaluated in the context of Pt.
An alternative plot and reordering of the data in Figure 2
making use of the Pt data gives perhaps a better picture
Scheme 1. Reagents: (a) imidazole, benzimidazole or pyrazole,
K2CO3, acetonitrile or DMF; (b) activated zinc, THF; 2-chloropyr-
imidine, (C6H5)2PCH2CH2P(C6H5)2]NiCl2; (c) LiOH, THF/MeOH/
H2O; (d) NH3, MeOH; (e) Raney–Ni, H2, EtOH/aqueous NH4OH; (f)
HCl/EtOH followed by NH3/EtOH; (g) NaN3, NH4Cl, DMF; (h)
SnCl2 DMF; (i) MeSO2Cl, NEt3, CH2Cl2/EtOH.

T. Fichert et al. / Bioorg. Med. Chem. Lett. 13 (2003) 719–722
721
of the relative effects of the various groups on perme-
ability. It is remarkable that even the most polar com-
pounds synthesized still retain moderate cell
permeability.
Figure 3 shows the relationship between cell perme-
ability and experimental distribution coefficients (log
D). Because of the nature of the scaffolds and function-
ality studied here, the log D ranges from ꢀ2.4 to 3. Pt is
plotted for compounds 14, 35, 37 and 39. Compounds with
log D values higher than 0and less than 3 fall in the highly
permeable class. Most of the compounds with log D values
below 0are moderately permeable, with the exception of
the amines 33 and 34 which display high permeability. This
classification is similar to one previously published for a
series of a structurally diverse drugs.2a
Table 1. Permeabilitya and log Db data
Compd
PCaco-2 ꢁ 106
PDR Pt ꢁ 106
Log
Doct/PBS
(cm/s)
(cm/s)
A to B (B to A)
68.1ꢂ1.2
1
2
4
5
6
8
1.78ꢂ0.25
1.01ꢂ0.04
ꢀ2.10ꢂ0.08
ꢀ2.37ꢂ0.11
2.91ꢂ0.05
2.47ꢂ0.01
ꢀ0.61ꢂ0.01
ꢀ1.13ꢂ0.11
ꢀ1.78ꢂ0.02
1.04ꢂ0.09
1.74ꢂ0.02
ꢀ1.65ꢂ0.02
ꢀ1.80ꢂ0.08
ꢂ0.03
67.8ꢂ2.2
0.67ꢂ0.02 (0.82ꢂ0.02)
0.71ꢂ0.05
1
7
0.75
0.33
Using the Caco-2 model we have evaluated the effect on
permeability of various functional groups commonly
seen in lead optimization efforts. For this set of com-
pounds we find a classification indicating high perme-
ability for compounds having log D values greater than
0(and less then 3) is seen, while compounds with log D
values lower than 0display variable permeability. Surpris-
ingly, compounds containing the tetrazole functionality
were found to be recognized by efflux pumps.
71.1ꢂ1.9
65.8ꢂ1.5
11
12
14
15
16
18
19
20
23
24
25
26
27
28
29
30
3.19ꢂ0.15
2.63ꢂ0.19
0.08ꢂ0.00 (0.58ꢂ0.02)
23.4ꢂ0.9
71.9ꢂ4.7
3.66ꢂ0.13
2.89ꢂ0.17
66.7ꢂ2.601.46
0.65ꢂ.05 (1.18ꢂ.03)
1.56ꢂ0.16 (5.21ꢂ.012)
2.93ꢂ0.21
2
3
0.92
3.4
ꢀ2.07ꢂ0.10
ꢀ0.72ꢂ0.11
ꢀ1.62ꢂ0.13
ꢀ1.98ꢂ0.12
ꢀ2.20ꢂ0.14
ꢀ0.01ꢂ0.10
1.70ꢂ0.02
0.71ꢂ0.05
ꢂ0.01
6.10ꢂ0.47
5.39ꢂ0.12
6.85ꢂ0.43
25.1ꢂ1.2
44.4ꢂ1.3
.28 31
34.6ꢂ1.00
32
33
34
35
36
37
38
39
40
41
27.6ꢂ1.1
0.21ꢂ0.03
ꢀ0.77ꢂ0.00
ꢀ1.11ꢂ0.03
ꢀ1.03ꢂ0.03
28.4ꢂ2.1
25.3ꢂ0.2
0.22ꢂ0.03 (0.60ꢂ0.03)
3
0.41
c
0.13ꢂ0.02 (23.4ꢂ2.3) 18012
0.14ꢂ0.01 (20.3ꢂ0.5) 145
0.11ꢂ0.01 (14.2ꢂ0.8) 129
Not determined
10
7.2
1.4
0.27ꢂ0.06
Not determinedc
ꢀ1.28ꢂ0.01
1.92ꢂ0.06
0.13ꢂ0.00 (2.63ꢂ0.11)
57.4ꢂ3.6
20
23.4ꢂ0.9
2.08ꢂ0.04
aValues are means of three experimentsꢂstandard deviation.
bLog D values were obtained using octanol and phosphate buffered
saline at pH 7.4. Values are means of six experiments ꢂ standard
deviation.
cCompound was not detected in the octanol phase.
Figure 2.
Figure 1.
Figure 3.

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T. Fichert et al. / Bioorg. Med. Chem. Lett. 13 (2003) 719–722
Stevenson, the compounds in this study are highly drug-like.
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ine Briggs for assistance in running the Caco-2 model
and the octanol/PBS distribution experiments. We also
thank Walter Davidson and Robert Harris for
determination of the HR-MS data.
1
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