DESIGN OF POTENT SELECTIVE ZINC-MEDIATED SERINE PROTEASE INHIBITORS

B. A. Katz, J. M. Clark, J. S. Finer-Moore, T. E. Jenkins, C. R. Johnson, M. J. Ross, C. Luong, W. R. Moore & R. M. Stroud^*. Nature 391, 608-612, 1998.

Axys Pharmaceuticals, Inc., 180 Kimball Way, S. San Francisco, CA 94080, USA and
*Department of Biochemistry, University of California, San Francisco, CA 94143, USA.
Brad_katz@axyspharm.com

Many serine proteases are targets for therapeutic intervention, but small molecule inhibitors of these targets often require chemically complex peptidomimetic or chiral structures whose high molecular weight frequently compromises oral bioavailability. Low molecular weight, non-peptide inhibitors of serine proteases utilizing reversible, high affinity scaffolds would offer a new chemical framework from which to develop potent and selective drugs for protease targets. Screening under various biochemical conditions identified bis(5-amidino-2-benzimidazolyl)-methane (BABIM) as one such inhibitor, standing out seemingly anomalously as the best inhibitor of trypsin (K_i = 1.7 x 10^-8 M) by a factor of > 100-fold in a series of over 60 relatively closely related analogs.¹ By probing the structural basis of potentiated inhibition, we discovered, using crystallographic methods,² a new mode of high affinity binding in which a Zn⁺² ion is tetrahedrally coordinated between two chelating nitrogens of BABIM and two active site residues, His-57 and Ser-195. Zn⁺², at sub-physiological levels, enhances inhibition by > 10³-fold. The distinct Zn⁺² coordination geometry coupled with the stability of the protease-Zn⁺²-inhibitor complex provides a high affinity, relatively rigid scaffold of reasonable molecular weight onto which substituents can be incorporated that enhance potency and/or selectivity through interactions with the target or anti-targets at regions where the sequences and structures of the proteases differ. This unique structural paradigm has been extended to numerous novel Zn⁺²-chelation scaffolds, enabling development of potent, highly selective, Zn⁺²-dependent inhibitors of several therapeutically important serine proteases, using a physiologically ubiquitous metal ion.

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1. Tidwell, R. R.; Geratz, J. D.; Dann, O.; Volz, G.; Zeh, D.; Loewe, H. J. Med. Chem., 1978, 21, 613.
2. Clark, J. M.; Jenkins, T. E.; Katz, B. A.; Stroud, R. M. U.S. Patent 5,693,515 (2 Dec 1997).