Merging allosteric and active site binding motifs: De novo generation of target selectivity and potency via natural-product-derived fragments

ChemMedChem

Volumn 10, Issue 3, 2015, Pages 451-454

  Lanz, Jan ^a   Ried, Rainer ^a  

^a ZURICH UNIVERSITY OF APPLIED SCIENCES   (Switzerland)

Author keywords

De novo drug design; Enzyme inhibitors; Fragment based drug discovery; Natural products; Structure activity relationships; Water mediated interactions

Indexed keywords

4 [[5 [2 [[(3 METHOXYPHENYL)METHYL]CARBAMOYL]ETH 1 YN 1 YL] 2,4 DIOXO 1,2,3,4 TETRAHYDROPYRIMIDIN 1 YL]METHYL]BENZOIC ACID; 4 [[5 [2 [[[3 (3 CARBOXYPROPOXY)PHENYL]METHYL] CARBAMOYL]ETH 1 YN 1 YL] 2,4 DIOXO 1,2,3,4 TETRAHYDROPYRIMIDIN 1 YL]METHYL]BENZOIC ACID; MATRIX METALLOPROTEINASE INHIBITOR; NATURAL PRODUCT; UNCLASSIFIED DRUG; URACIL DERIVATIVE; BIOLOGICAL PRODUCT; COLLAGENASE 3; ENZYME INHIBITOR;

ALKYLATION; ALLOSTERISM; ARTICLE; BINDING AFFINITY; BIOLOGICAL ACTIVITY; CRYSTAL STRUCTURE; DRUG BINDING SITE; DRUG DESIGN; DRUG POTENCY; DRUG SELECTIVITY; DRUG STRUCTURE; DRUG SYNTHESIS; IC50; MODULATION; PRIORITY JOURNAL; BINDING SITE; CHEMISTRY; ENZYME ACTIVE SITE; HUMAN; METABOLISM; MOLECULAR DOCKING;

ALLOSTERIC SITE; BIOLOGICAL PRODUCTS; CATALYTIC DOMAIN; DRUG DESIGN; ENZYME INHIBITORS; HUMANS; MATRIX METALLOPROTEINASE 13; MATRIX METALLOPROTEINASE INHIBITORS; MOLECULAR DOCKING SIMULATION;

EID: 84923362153     PISSN: 18607179     EISSN: 18607187     Source Type: Journal    
DOI: 10.1002/cmdc.201402478     Document Type: Article

References (50)

1. a) T. Rodrigues, T. Kudoh, F. Roudnicky, Y. F. Lim, Y.-C. Lin, C. P. Koch, M. Seno, M. Detmar, G. Schneider, Angew. Chem. Int. Ed. 2013, 52, 10006-10009;
2. Angew. Chem. 2013, 125, 10190-10193;
3. b) E. A. Meyer, R. Brenk, R. K. Castellano, M. Furler, G. Klebe, F. Diederich, ChemBioChem 2002, 3, 250-253;
4. c) J. Besnard, G. F. Ruda, V. Setola, K. Abecassis, R. M. Rodriguiz, X.-P. Huang, S. Norval, M. F. Sassano, A. I. Shin, L. A. Webster, F. R. C. Simeons, L. Stojanovski, A. Prat, N. G. Seidah, D. B. Constam, G. R. Bickerton, K. D. Read, W. C. Wetsel, I. H. Gilbert, B. L. Roth, A. L. Hopkins, Nature 2012, 492, 215-220.
5. a) A. L. Harvey, Drug Discovery Today 2008, 13, 894-901;
6. b) D. J. Newman, G. M. Cragg, J. Nat. Prod. 2012, 75, 311-335.
7. a) G. M. Cragg, P. G. Grothaus, D. J. Newman, J. Nat. Prod. 2014, 77, 703-723;
8. b) A. Ganesan, Curr. Opin. Chem. Biol. 2008, 12, 306-317;
9. c) S. Wetzel, A. Schuffenhauer, S. Roggo, P. Ertl, H. Waldmann, Chimia 2007, 61, 355-360;
10. d) S. Wetzel, R. S. Bon, K. Kumar, H. Waldmann, Angew. Chem. Int. Ed. 2011, 50, 10800-10826;
11. Angew. Chem. 2011, 123, 10990-11018.
12. a) D. A. Erlanson, Top. Curr. Chem. 2012, 317, 1-32;
13. b) P. J. Hajduk, J. Greer, Nat. Rev. Drug Discovery 2007, 6, 211-219;
14. c) C. W. Murray, D. C. Rees, Nat. Chem. 2009, 1, 187-192;
15. d) A. Ciulli, C. Abell, Curr. Opin. Biotechnol. 2007, 18, 489-496;
16. e) C. Abad-Zapatero, Expert Opin. Drug Discovery 2007, 2, 469-488.
17. B. Over, S. Wetzel, C. Grütter, Y. Nakai, S. Renner, D. Rauh, H. Waldmann, Nat. Chem. 2013, 5, 21-28.
18. Molecular Operating Environment (MOE), Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, H3A2R7 (Canada), 2013.
19. E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, T. E. Ferrin, J. Comput. Chem. 2004, 25, 1605-1612.
20. A. R. Johnson, A. G. Pavlovsky, D. F. Ortwine, F. Prior, C.-F. Man, D. A. Bornemeier, C. A. Banotai, W. T. Mueller, P. McConnell, C. Yan, V. Baragi, C. Lesch, W. H. Roark, M. Wilson, K. Datta, R. Guzman, H.-K. Han, R. D. Dyer, J. Biol. Chem. 2007, 282, 27781-27791.
21. a) C. M. Overall, C. López-Otín, Nat. Rev. Cancer 2002, 2, 657-672;
22. b) M. Shah, D. Huang, T. Blick, A. Connor, L. A. Reiter, J. R. Hardink, C. C. Lynch, M. Waltham, E. W. Thompson, PLoS One 2012, 7, e29615;
23. c) K. Kessenbrock, V. Plaks, Z. Werb, Cell 2010, 141, 52-67;
24. d) I. Stamenkovic, Semin. Cancer Biol. 2000, 10, 415-433;
25. e) L. Blavier, A. Lazaryev, F. Dorey, G. M. Shackleford, Y. A. DeClerck, Cancer Res. 2006, 66, 2691-2699;
26. f) M. Egeblad, Z. Werb, Nat. Rev. Cancer 2002, 2, 161-174.
27. a) G. Murphy, H. Nagase, Nat. Clin. Pract. Rheumatol. 2008, 4, 128-135;
28. b) V. M. Baragi, G. Becher, A. M. Bendele, R. Biesinger, H. Bluhm, J. Boer, H. Deng, R. Dodd, M. Essers, T. Feuerstein, B. M. Gallagher, Jr., C. Gege, M. Hochguertel, M. Hofmann, A. Jaworski, L. Jin, A. Kiely, B. Korniski, H. Kroth, D. Nix, B. Nolte, D. Piecha, T. S. Powers, F. Richter, M. Schneider, C. Steeneck, I. Sucholeiki, A. Taveras, A. Timmermann, J. Van Veldhuizen, J. Weik, X. Wu, B. Xia, Arthritis Rheum. 2009, 60, 2008-2018;
29. c) N.-G. Li, Z.-H. Shi, Y.-P. Tang, Z.-J. Wang, S.-L. Song, L.-H. Qian, D.-W. Qian, J.-A. Duan, Curr. Med. Chem. 2011, 18, 977-1001;
30. d) V. La Pietra, L. Marinelli, S. Cosconati, F. S. Di Leva, E. Nuti, S. Santamaria, I. Pugliesi, M. Morelli, F. Casalini, A. Rosello, C. La Motta, S. Taliani, R. Visse, H. Nagase, F. De Settimo, E. Novellino, Eur. J. Med. Chem. 2012, 47, 143-152;
31. e) S. J. Taylor, A. Abeywardane, S. Liang, I. Muegge, A. K. Padyna, Z. Xiong, M. Hill-Drzewi, B. Farmer, X. Li, B. Collins, J. X. Li, A. Heim-Reither, J. Proudfoot, Q. Zhang, D. Goldberg, L. Zuvela-Jelaska, H. Zaher, J. Li, N. A. Farrow, J. Med. Chem. 2011, 54, 8174-8187.
32. a) A. Júngel, C. Ospelt, M. Lesch, M. Thiel, T. Sunyer, O. Schorr, B. A. Michel, R. E. Gay, C. Kolling, C. Flory, S. Gay, M. Neidhart, Ann. Rheum. Dis. 2010, 69, 898-902;
33. b) B. A. Moore, S. Aznavoorian, J. A. Engler, L. J. Windsor, Biochim. Biophys. Acta Mol. Basis Dis. 2000, 1502, 307-318.
34. a) H. Nagase, R. Visse, G. Murphy, Cardiovasc. Res. 2006, 69, 562-573;
35. b) J. T. Peterson, Cardiovasc. Res. 2006, 69, 677-687;
36. c) M. J. Sierevogel, G. Pasterkamp, D. P. V. de Kleijn, B. H. Strauss, Curr. Pharm. Des. 2003, 9, 1033-1040.
37. G. A. Rosenberg, Lancet Neurol. 2009, 8, 205-216.
38. a) H. Nagase, R. Visse in Drug Design of Zinc-Enzyme Inhibitors (Eds.: C. T. Supuran, J.-Y. Winum), Wiley, Hoboken, 2009, pp. 489-517;
39. b) D. Sbardella, G. F. Fasciglione, M. Gioia, C. Ciaccio, G. R. Tundo, S. Marini, M. Coletta, Mol. Aspects Med. 2012, 33, 119-208.
40. J. A. Sparano, P. Bernardo, P. Stephenson, W. J. Gradishar, J. N. Ingle, S. Zucker, N. E. Davidson, J. Clin. Oncol. 2004, 22, 4683-4690.
41. a) T. Fischer, R. Riedl, ChemMedChem 2013, 8, 1457-1461;
42. b) C. K. Engel, B. Pirard, S. Schimanski, R. Kirsch, J. Habermann, O. Klingler, V. Schlotte, K. U. Weithmann, K. U. Wendt, Chem. Biol. 2005, 12, 181-189;
43. c) C. De Savi, A. D. Morley, I. Nash, G. Karoutchi, K. Page, A. Ting, S. Gerhardt, Bioorg. Med. Chem. Lett. 2012, 22, 271-277;
44. d) C. Gege, B. Bao, H. Bluhm, J. Boer, B. M. Gallagher, B. Korniski, T. S. Powers, C. Steeneck, A. G. Taveras, V. M. Baragi, J. Med. Chem. 2012, 55, 709-716;
45. e) M. E. Schnute, P. M. O'Brien, J. Nahra, M. Morris, W. H. Roark, C. E. Hanau, P. G. Ruminski, J. A. Scholten, T. R. Fletcher, B. C. Hamper, J. N. Carroll, W. C. Patt, H. S. Shieh, B. Collins, A. G. Pavlovsky, K. E. Palmquist, K. W. Aston, J. Hitchcock, M. D. Rogers, J. McDonald, A. R. Johnson, G. E. Munie, A. J. Wittwer, C.-F. Man, S. L. Settle, O. Nemirovskiy, L. E. Vickery, A. Agawal, R. D. Dyer, T. Sunyer, Bioorg. Med. Chem. Lett. 2010, 20, 576-580.
46. a) R. Chinchilla, C. Najera, Chem. Rev. 2007, 107, 874-922;
47. b) K. Sonogashira, J. Organomet. Chem. 2002, 653, 46-49.
48. JChem for Excel (version 6.1.5.781), ChemAxon, www.chemaxon.com, 2013.
49. P. Willett, Drug Discovery Today 2006, 11, 1046-1053.
50. J. J. Li, A. R. Johnson, Med. Res. Rev. 2011, 31, 863-894.