C O M M U N I C A T I O N S
In summary, selection of heterocycles to optimize potency is a
central activity in the pursuit of therapeutic agents. The present
study clearly demonstrates the utility of FEP calculations for guiding
these efforts in the context of structure-based drug design and for
providing insights into the origins of variations in activity. Diverse
sets of candidate heterocycles can be screened in parallel in a few
days before committing to synthesis. The current application led
to compounds 5, 6, and 11, which are novel, highly potent inhibitors
of HIV-RT with greater than 1000-fold safety margins (CC50/EC50).
Acknowledgment. Gratitude is expressed to the National
Institutes of Health (Grants AI44616, GM32136, GM35208,
GM49551) for support.
Figure 2. Last configuration from a MC simulation of 11 bound to HIV-
RT. Carbon atoms of 11 are gold; H-bonds with Lys101 are highlighted.
Six water molecules are H-bonded to Glu138. Ca. 6500 atoms are hidden.
Supporting Information Available: 1H, 13C spectral data of
NNRTIs in Table 1, and synthetic details for the heteroaryl chlorides
13. This material is available free of charge via the Internet at http://
pubs.acs.org.)
though they are relatively cytotoxic (Table 1). Compounds 5 and
6 are equipotent; the added nitrogen in 6 is well-accommodated in
the bound structure (Figure 1), but it is also fully solvent-exposed
unbound. They are far more potent than nevirapine (Viramune) and
similar in potency to efavirenz (Sustiva). Compounds 5 and 6 are
also more potent than their progenitors 3 and 4. This outcome was
not obvious owing to the following: (1) narrowing of the activity
funnel, that is, 3 and 4 are already potent; (2) the conversions
effectively embody a 2-pyrimidine to 2-pyridine change, which is
unfavorable on the basis of prior results for 2 (0.2 µM) and its
pyridine analog (3.2 µM);1 (3) 5 and 6 with QPlogS values1 of
-4.9 and -4.7 are predicted to be 0.2 log unit more soluble in
water than 3 and 4.
The computed/experimental comparison is particularly good for
the isomers 9, 10, and 11, which provide a striking example of the
sensitivity of activity to structure. Compound 9 is a weak inhibitor
because all hydrogen bonding with the pyrrolyl NH is lost upon
binding. From the ∆G results for the unbound and bound legs
of the FEP calculations, the greater potency for 11 than 10 stems
from better interactions with the protein rather than poorer hydra-
tion unbound. The average energy components confirm that the
interaction with HIV-RT is more favorable for 11 than 10 by 6.0
kcal/mol, while the interaction in water is only more favorable by
3.3 kcal/mol. The variation comes entirely from the Coulombic
energy components, and the average dipole moment for bound 11
is 3.8 D, while it is 2.0 D for 10. At least part of the difference
could be interpreted to reflect greater contribution from resonance
structure 16 for 11 than from 17 for 10. CM1A charges10 scaled
by 1.14 have been used here for the inhibitors;5 for the aza N and
bridgehead N they are -0.44 and +0.01 e for 11 and -0.38 and
-0.22 e for 10. The greater negative charge on the aza N of 11
strengthens the hydrogen bond with the backbone NH of Lys101
(Figure 2). The hydrogens on C5 and C6 in 11 are also more
positive than the corresponding ones in 10, which makes interaction
with Glu138 more favorable. In the absence of the computational
results, prediction of the significantly greater activity of 11 would
be elusive, particularly since pyrimidine 2 is far more active than
the corresponding pyridine and pyrazine.1
References
(1) Jorgensen, W. L.; Ruiz-Caro, J.; Tirado-Rives, J.; Basavapathruni, A.;
Anderson, K. S.; Hamilton, A. D. Bioorg. Med. Chem. Lett. 2006, 16,
663-667.
(2) Ruiz-Caro, J.; Basavapathruni, A.; Kim, J. T.; Wang, L.; Bailey, C. M.;
Anderson, K. S.; Hamilton, A. D.; Jorgensen, W. L. Bioorg. Med. Chem.
Lett. 2006, 16, 668-671.
(3) Thakur, V. V.; Kim, J. T.; Hamilton, A. D.; Bailey, C. M.; Domaol, R.
A.; Wang, L.; Anderson, K. S.; Jorgensen, W. L. Bioorg. Med. Chem.
Lett. 2006, 16, 5664-5667.
(4) Initial structures for the inhibitors and complexes were built with the
BOMB program and included 159 residues of HIV-RT. A total of 1250
and 2000 TIP4P water molecules were added in 25 Å caps for the
complexes and unbound ligands, respectively. Each FEP utilized 20 free
energy increments and typically covered 20 × 106 (20 M) configurations
for equilibration and 40 M configurations for averaging. The OPLS-AA
force field was used for the protein and OPLS/CM1A for the inhibitors,
and the MC/FEP calculations were performed with MCPRO 2.0. Details
on the BOMB and FEP calculations can be found in ref 1.
(5) Jorgensen, W. L.; Tirado-Rives, J. Proc. Natl. Acad. Sci. U.S.A. 2004,
102, 6665-6670.
(6) Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1689-
1700.
(7) Representative procedure (5): 4-Chloro-furo[3,2-c ]pyridine (169 mg, 1.1
mmol), 5-amino-2-chlorophenol (149 mg, 1.04 mmol), and 37% HCl (108
µL, 1.09 mmol) in 10% aqueous EtOH solution were stirred at 90 °C for
12 h. The reaction mixture was diluted with EtOAc and washed with
aqueous NaHCO3 solution and brine. The organic phase was separated,
dried over anhydrous Na2SO4, and concentrated under reduced pressure.
The crude product was purified by flash silica gel chromatography with
20% EtOAc in hexanes to give 2-chloro-5-(furo[3,2-c ]pyridine-4-
ylamino)phenol (237 mg, 83% yield). This material (237 mg, 0.91 mmol)
and Cs2CO3 (356 mg, 1.09 mmol) in acetone (5 mL) were treated with
3,3-dimethylallyl bromide (117 µL, 1.0 mmol) at room temperature. After
2 h, the reaction mixture was diluted with EtOAc and washed with aqueous
NH4Cl solution and brine. The organic phase was separated, dried, and
concentrated as above. Purification by flash silica gel chromatography
with 10% EtOAc in hexanes gave 5 (281 mg, 94% yield).
(8) Activities against the IIIB strain of HIV-1 were determined using MT-2
human T-cells; the EC50 dose yields 50% protection of infected cells using
the MTT method. The CC50 for inhibition of MT-2 cell growth by 50%
was obtained simultaneously: Ray, A. S.; Yang, Z.; Chu, C. K.; Anderson,
K. S. Antimicrob. Agents Chemother. 2002, 46, 887-891.
(9) Rizzo, R. C.; Udier-Blagovic´, M.; Wang, D.-P.; Watkins, E. K.; Smith,
M. B. K.; Smith, R. H.; Tirado-Rives, J.; Jorgensen, W. L. J. Med. Chem.
2002, 45, 2970-2987 (see page 2976).
(10) Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. J. Comput.
Aided Mol. Des. 1995, 9, 87-110.
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