Journal of Medicinal Chemistry
Article
ranked models for both TbrPDEB1 and TbrPDB2 were based on
LmjPDEB1 as the template. Multiple modeling evaluation tools were
used to confirm the quality of the model structures, including
PROCHECK,28 MolProbity,29 and Verify3D,30 described in detail in
the Supporting Information.
2H), 7.32 (d, J = 7.2 Hz, 1H), 6.97 (d, J = 8 Hz, 1H), 5.21 (s, 2H),
3.95 (s, 3H). LCMS found 403.01 [M + H]+.
N-(3,5-Dichloropyridin-4-yl)-3,4-diethoxybenzamide (16). Yield:
1
50%. H NMR (400 MHz, CDCl3) δ 8.54 (s, 2H), 7.71 (s, 1H),
7.51−7.47 (m, 2H), 6.92 (d, J = 8.0 Hz, 1H), 4.16 (m, 4H), 1.48 (m,
6H). LCMS found 355.01 [M + H]+.
Piclamilast Docking. The model TbPDEB1 structures were
further processed using the Maestro 9.1 protein preparation wizard
(Schrodinger, LLC, 2010, New York, NY). A restrained minimization
of the protein structure was performed using the default constraint of
0.3 Å rmsd and OPLS 2001 force field. The 3D coordinates of
piclamilast (1) were then generated using the ligprep utility in Maestro
9.0. The docking parameters were first examined by replication of the
crystal structures of the PDE4D/roflumilast complex (PDB ID
1XOQ) and the PDE4B/rolipram complex (PDB ID 1XMY).21
Docking was performed with Glide version 3.5 in standard precision
(SP) mode. The docking experiments were conducted with the
constraint that at least one H-bond must be formed between the
ligand and conserved Gln in the P clamp.
4-((3,5-Dichloropyridin-4-yl)carbamoyl)-2-methoxyphenyl Ace-
1
tate (17). Yield: 45%. H NMR (400 MHz, CDCl3) δ 8.57 (s, 2H),
7.71 (s, 1H), 7.60 (m, 1H), 7.50 (d, J = 8.0 Hz, 1H), 7.18 (d, J = 8.0
Hz, 1H), 3.93 (s, 3H), 2.35 (s, 3H). LCMS found 355.01 [M + H]+.
2-Chloro-N-(3,5-dichloropyridin-4-yl)-3,4-dimethoxybenzamide
1
(18). Yield: 49%. H NMR (400 MHz, CDCl3) δ 8.55 (s, 2H), 8.25
(s, 1H), 7.71 (d, J = 8.8 Hz, 1H), 6.93 (d, J = 8.8 Hz, 1H), 3.94 (s,
3H), 3.89 (s, 3H). LCMS found 361.01 [M + H]+.
2-Chloro-N-(3,5-dichloropyridin-4-yl)-4,5-dimethoxybenzamide
1
(19). Yield: 51%. H NMR (500 MHz, DMSO-d6) δ 10.65 (s, 1H),
8.73 (s, 2H), 7.41 (s, 1H), 7.13 (d, J = 7.5 Hz, 1H), 3.82 (s, 3H), 3.80
(s, 3H). LCMS found 361.01 [M + H]+.
Chemical Synthesis. Unless otherwise noted, reagents were
obtained from Sigma-Aldrich, Inc. (St. Louis, MO) or ASDI, Inc.
(Newark, DE), and used as received. Reaction solvents were purified
by passage through alumina columns on a purification system
manufactured by Innovative Technology (Newburyport, MA). NMR
spectra were obtained Varian NMR systems, operating at 400 or 500
MHz for 1H acquisitions as noted. LCMS analysis was performed
using a Waters Alliance reverse-phase HPLC, with single-wavelength
UV−visible detector and LCT Premier time-of-flight mass spectrom-
eter (electrospray ionization). All newly synthesized compounds were
deemed >95% pure by LCMS analysis prior to submission for
biological testing.
ASSOCIATED CONTENT
■
S
* Supporting Information
A tabulation of all the benchmarked human PDE inhibitors,
with their references and screening Data, also publically
a v a i l a b l e a s
a
s h a r e d d a t a s e t a t w w w .
TbrPDEB1 and B2 and alignment between TbrPDEB1, B2,
LmjPDEB1, and hPDE4D. This material is available free of
General Procedure. Various substituted benzoic acids (0.2 mmol)
were obtained in preweighed quantities in 8 mL screw cap vials. To the
acid (1 equiv) was added 3 mL of thionyl chloride, and the mixture
was agitated on a heated shaker plate at 90 °C for 3 h. The crude
mixture was concentrated using a Genevac evaporator, and residual
thionyl chloride was azeotropically removed with 2−3 sequential
additions and evaporations of toluene. In a separate, flame-dried flask,
3,5-dichloropyridin-4-amine (0.75 equiv) was dissolved in dry THF
and then added dropwise to sodium hydride (2 equiv) in dry THF
(0.1 M final concentration) under an inert atmosphere at 0 °C. The
mixture was allowed to warm to room temperature and was stirred for
2 h and cooled once again to 0 °C. The acid chloride prepared above
was dissolved in THF (0.1 M final concentration) and added dropwise
to the aminopyridine suspension, and the reaction mixture was stirred
for 24 h at room temperature. The solvent was removed by
evaporation, and the residue was taken up in EtOAc. The organic
layer was washed with 1 M HCl (1×), then NaHCO3 (3×), and dried
over Na2SO4. The desired products were isolated following
purification via silica gel chromatography (EtOAc/hexanes gradient).
N-(3,5-Dichloropyridin-4-yl)-3,4,5-trimethoxybenzamide (9).
AUTHOR INFORMATION
■
Corresponding Author
ACKNOWLEDGMENTS
■
Funding from the National Institutes of Health (R01AI082577,
including an ARRA summer supplement), the National Science
Foundation (MCB-0843603), Northeastern University, Boston
University, and gift of sildenafil from Pfizer, Inc. are gratefully
acknowledged.
ABBREVIATIONS USED
■
HAT, human African trypanosomiasis; BF, bloodstream form
T. brucei; cAMP, cyclic adenosine monophosphate; cGMP,
cyclic guanosine monophosphate; PDB, Protein Data Bank;
PDE, phosphodiesterase; TbrPDEB1, PDEB1 of Trypanosoma
brucei; TbrPDEB2, PDEB2 of Trypanosoma brucei; CNS,
central nervous system; NTD, neglected tropical disease;
EHNA, erythro-9-(2-hydroxy-3-nonly)adenine
1
Yield: 54%. H NMR (400 MHz, CDCl3) δ 8.60 (s, 2H), 7.78 (s,
1H), 7.22 (s, 2H), 3.08 (s, 9H). LCMS found 357.01 [M + H]+.
N-(3,5-Dichloropyridin-4-yl)-3-ethoxy-4-methoxybenzamide
1
(11). Yield: 12%. H NMR (500 MHz, CDCl3) δ 8.56 (s, 2H), 7.64
REFERENCES
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(br, 1H), 7.52 (s, 1H), 7.5 (m, 1H), 6.95 (d, J = 8.0 Hz, 1H), 4.21 (q,
2H), 3.96 (s, 3H), 1.50 (t, J = 7.0 Hz, 3H). LCMS found 341.01 [M +
H]+.
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(13). Yield: 37%. H NMR (400 MHz, CDCl3) δ 8.54 (s, 2H), 7.71
(s, 1H), 7.53 (m, 1H), 7.50 (d, J = 2.0 Hz, 1H), 6.94 (d, J = 8.8 Hz,
1H), 4.64 (m, 1H), 3.93 (s, 3H), 1.40 (d, J = 6.0 Hz, 6H). LCMS
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3-(Benzyloxy)-N-(3,5-dichloropyridin-4-yl)-4-methoxybenzamide
1
(15). Yield: 22%. H NMR (400 MHz, CDCl3) δ 8.54 (s, 2H), 7.59
(s, 1H), 7.53 (m, 2H), 7.46 (d, J = 7.2 Hz, 2H), 7.37 (t, J = 7.2 Hz,
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dx.doi.org/10.1021/jm201148s|J. Med. Chem. 2011, 54, 8188−8194