CHEMMEDCHEM
COMMUNICATIONS
DOI: 10.1002/cmdc.201300278
Strategic Targeting of Multiple Water-Mediated
Interactions: A Concise and Rational Structure-Based
Design Approach to Potent and Selective MMP-13
Inhibitors
Thomas Fischer and Rainer Riedl*[a]
In memoriam Claudia Nothnagel
Water is an essential molecule in biological systems based on
its role as the solvent for life.[1] Understanding the dynamics of
the interaction between water and proteins represents
a highly active field of research in molecular recognition,
chemical biology, and drug discovery.[2,3] In chemical biology,
water-mediated interactions offer tremendous opportunities
for the development of novel chemical structures with biologi-
cal activity, but due to its small size on the one hand and to its
overwhelming abundance as a solvent on the other hand,
water is often neglected when it comes to the detailed study
of biological processes on a molecular or atomic level. Here,
we report the very efficient use of X-ray crystallographic data
containing structural water molecules for the design and syn-
thesis of potent and selective matrix metalloproteinase-13
(MMP-13) inhibitors by targeting multiple water-mediated
interactions between the protein target and the inhibitor.
MMP-13 is a highly relevant and validated target for a multi-
tude of severe diseases, such as cancer, osteoarthritis and rheu-
matoid arthritis.[4] MMP-13 is a member of the zinc-dependent
endopeptidase family. It is the dominant MMP involved in
type II collagen cleavage in the degradation process of extra-
cellular matrix during growth and tissue remodeling.[4b,5,6] Early
attempts at finding inhibitors against MMPs resulted in pepti-
domimetics derived from natural substrates with modified moi-
eties close to the scissile amide bond.[4g] The potency of these
inhibitors was further enhanced by introducing zinc-chelating
groups in order to bind to the zinc ion in the active site of the
enzyme. Hydroxamates turned out to be the most efficient
zinc binders.[7,8] Because of unsatisfying bioavailability and
severe side effects due to a lack of selectivity, all clinical candi-
dates containing strong zinc binding groups failed in clinical
trials.[9] While doxycycline, an antibiotic tetracycline that exhib-
its off-target MMP inhibition, has been the only inhibitor to
reach the market so far, this does indicate that the target pro-
tein family is indeed druggable.[4g] In order to overcome the
deleterious side effects of strong zinc binding inhibitors, a new
class of MMP inhibitors has been developed recently that does
not bind to the catalytic zinc but rather binds deep within the
S1’ pocket.[10] This finding leads to new opportunities for the
discovery of selective MMP-13 inhibitors based on the structur-
al differences in the S1’ binding site among different MMPs.
In chemical biology and medicinal chemistry, there is a con-
stant need for novel small molecules modulating biological ac-
tivity in order to achieve insights into the underlying biological
processes on a molecular level. In particular, pharmaceutical
companies spend a considerable amount of their budget in
the development of potent and selective scaffolds of biologi-
cally active molecules. Those small-molecule modulators can
either be discovered by extensive and resource-intensive
screening campaigns or by rational design approaches. Rather
than performing screening activities, we approached this prob-
lem by analyzing co-crystal structures of the target protein in-
cluding structural water molecules in order to define the phar-
macophore and substitution pattern for inhibitor scaffolds.
Here, our focus was on using structural water molecules as
binding partners for novel small-molecule modulators.
Analysis of the co-crystal structure PDB 2OW9[10h] (Figure 1)
allowed us to design a novel scaffold of MMP-13 inhibitors
[a] T. Fischer, Prof. Dr. R. Riedl
Institute for Chemistry and Biological Chemistry
Zurich University of Applied Sciences (ZHAW)
Einsiedlerstrasse 31, 8820 Wꢀdenswil (Switzerland)
Supporting information for this article is available on the WWW under
ꢀ 2013 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
reproduction in any medium, provided the original work is properly
cited and is not used for commercial purposes.
Figure 1. Analyzing the pharmacophore of the co-crystallized inhibitor in
PDB 2OW9[10h] allowed for the generation of novel phthalimide scaffold 4.
ꢀ 2013 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim ChemMedChem 2013, 8, 1457 – 1461 1457