M. Pompei et al. / Bioorg. Med. Chem. Lett. 19 (2009) 2574–2578
2577
Figure 3. Compounds 13, 15 and 2 docked in the protease binding site, derived
from full-length NS3 protein. Colour code: compound 13 (yellow); compound 15
(blue); compound 2 (green). Oxygen atoms (red), P atoms (orange).
Figure 4. Detail of the P1 region of the P2–P4 phosphorous macrocycles. Super-
position of compounds 13, 15 and 2 and hydrogen bonds in the oxyanion hole and
with the catalytic His57.
Accordingly the significant boost in potency observed for 13 and 15
in comparison to 14 might be in part related to the increased acid-
ity of the P1 phosphorous replacement (pKa = 2.3 and 3.1, respec-
tively). Interestingly, these values are also the closest within the
series to those of the carboxylic acid 2 (pKa = 3.4). These observa-
tions are in agreement with previous studies which highlighted
the importance of an acidic group in P1 with a value of pKa close
to that of the carboxylic function.22
carboxylic acid 2. With the support of the modeling studies here
presented, further work is on-going to explore additional elabora-
tion of the phosphinate moiety in combination with structural
modification within the macrocycle. Results will be reported in
due course.
Acknowledgements
Recent X-ray crystal structures of product inhibitors with a P1
terminal carboxylic acid23 and docking studies of P1 acylsulfona-
mide inhibitors22 bound to the HCV–NS3/4A complex have eluci-
dated the interactions between the protease domain and these
acidic functions and given some insight into their mechanism of
action. Our additional interest in this potent class of novel phos-
phorous inhibitors is given by the alkyl-group present in the phos-
phonate moiety which might offer a handle towards further
elaboration to optimize interactions within the active site of
HCV–NS3 protease and achieve fine tuning of the physicochemical
properties. In order to further strengthen our hypothesis, the single
stereoisomers of 13 and 15 with the same relative configuration at
the cyclopropryl junction of the analogue 2, have been modeled
into the active site of the HCV–NS3 protease (Fig. 3).
The superposition shows that the phosphonate moiety is capa-
ble of forming the typical hydrogen bond in the oxyanion cavity
and to the catalytic His57 (Fig. 4). Its binding mode is similar to
that of the product inhibitor carboxylate 2. Due to its steric
requirements and not being good hydrogen bond acceptor the
methyl group of compound 15 is oriented towards the open region
of the catalytic site.
This atomic view of the binding mode of our P1 phosphorous
inhibitors, combined with the observed inhibitory potency, high-
lights the overall good biososteric profile of the P1 acidic phospho-
rous framework. Moreover, the promising orientation of the
methyl group of compound 15 towards the open region of the cat-
alytic site supports the exploitation of further modifications of the
phosphinate P1 fragment to gain in additional interactions within
the NS3 protease.
In summary, this work identified a novel class of P2–P4 macro-
cyclic inhibitors of HCV–NS3 protease bearing phosphorous acid
groups in P1. The optimal compound showed nanomolar enzyme
inhibition and sub-micromolar potency in the cell based assay.
The most active analogues were the methyl-phosphinates 15 char-
acterized by a calculated pKa value close to that of the parent
We thank Silvia Pesci for structural assignment and Sergio
Altamura, Jillian DiMuzio, Monica Bisbocci, Ottavia Cecchetti and
Nadia Gennari for biological testing.
References and notes
1. (a) WHO Weekly Epidemiol. Rec. 1999, 74, 425; (b) Modi, A. A.; Hoofnagle, J. H.
Hepatology 2007, 46, 615.
2. (a) Pearlman, B. L. Am. J. Med. 2004, 117, 344; (b) Manns, M. P.; Wedmeyer, H.;
Cornberg, M. Gut 2006, 55, 1350.
3. Reed, K. E.; Rice, C. M. In Hepatitis C Virus; Reesink, H. W., Ed.; Karger: Basel,
Switzerland, 1998; p 55.
4. (a) Gordon, C. P.; Keller, P. A. J. Med. Chem. 2005, 48, 1; (b) Cross, T.; Antoniades,
C.; Harrison, P. Postgraduate Med. J. 2008, 84, 990; (c) Jensen, D.; Ascione, A.
Antiv. Ther. 2008, 13, 31.
5. (a) Chen, S. H.; Tan, S. L. Curr. Med. Chem. 2005, 12, 2317; (b) Thomson, J. A.;
Perni, R. B. Curr. Opin. Drug Discovery Dev. 2006, 9, 606.
6. (a) Llinas-Brunet, M.; Bailey, M.; Bolger, G.; Brochu, C.; Faucher, A. J. Med. Chem.
2004, 47, 1605; (b) Lamarre, D.; Anderson, P.; Bailey, M.; Beaulieu, P.; Bolger, G.
Nature 2003, 42, 1356.
7. Goudreau, N.; Llinas-Brunet, M. Expert Opin. Investig. Drugs 2005, 14, 1129.
8. (a) Narjes, F.; Koehler, K.; Koch, U.; Gerlach, B. Bioorg. Chem. Lett. 2002, 12, 701;
(b) Yip, Y.; Victor, F.; Lamar, J. Bioorg. Med. Chem. Lett. 2004, 14, 5007; (c)
Venkataman, S.; Bogen, S.; Arasappan, A.; Bennet, F. J. Med. Chem. 2006, 49, 6074.
9. (a) Johansson, A.; Poliakov, A.; Akerblom, E. Bioorg. Med. Chem. 2003, 11, 2551;
(b) Rancourt, J.; Cameron, D.; Lamarre, D. J. Med. Chem. 2004, 47, 2511; (c) Rönn,
R.; Sabnis, Y.; Gossas, T. Bioorg. Med. Chem. 2006, 14, 544; (d) Örtqvist, P.;
Peterson, S.; Kerblom, E. Bioorg. Med. Chem. 2007, 15, 1448.
10. Liverton, N. J.; Holloway, K.; McCauley, J.; Butcher, J. J. Am. Chem. Soc. 2008, 130,
4607.
11. McCauley, J. A. Abstract of papers, 235th ACS National Meeting, New Orleans,
LA, USA, April 6–10, 2008.
12. (a) Campbell, J. A. WO 02/060926, 2002.; (b) Wang, X. A. WO 03/099274, 2003.;
(c) Campbell, J. A. WO 03/053349, 2003.; (d) Campbell, J. A. WO 03/099316,
2003.; (e) Ripka, A. US 04/0048802, 2004.; (f) Campbell, J. A. US 04/0077551,
2004.
13. (a) Chen, X.; Wang, W. Annu. Rep. Med. Chem. 2003, 38, 333; (b) Patani, G. A.;
LaVoie, E. Chem. Rev. 1996, 96, 3147.
14. (a) Chaudhary, K. WO 06/020276, 2006.; (b) Casarez, A. WO 08/005565, 2008.
15. Vermuth, C. G. In The Practice of Medicinal Chemistry; Academic Press, 1996.
16. Pelliciari, R. J. Mol. Graphics ModelL. 2007, 26, 728.
17.
L-Tartaric resolution of the amine 5 was tried but with unsuccessful results.
18. Liverton, N. J. WO 08/051477, 2008.
19. Poliakov, A.; Hubatsch, I.; Shuman, C.; Stenberg, G. Protein Expr. Purif. 2002, 25, 363.