Communications
DOI: 10.1002/anie.201001343
Multicomponent Reactions
Robust Generation of Lead Compounds for Protein–Protein
Interactions by Computational and MCR Chemistry:
p53/Hdm2 Antagonists**
Anna Czarna, Barbara Beck, Stuti Srivastava, Grzegorz M. Popowicz, Siglinde Wolf,
Yijun Huang, Michal Bista, Tad A. Holak, and Alexander Dꢀmling*
In memory of Ivar Ugi
The discovery of a lead compound is an essential process in
early drug discovery, hopefully eventually resulting in a
clinical candidate and a drug for the treatment of a disease.
Besides affinity and selectivity for the target, however, other
target-unrelated compound properties are equally important
for the fate of a drug candidate, for example, water solubility,
lipophilicity, and molecular weight since they determine
important aspects such as oral bioavailability, dosing sched-
ule, and side effects. The parallel discovery and early
development of several leads is therefore now pursued
whenever possible, an approach that takes into account the
high attrition rate of early drug discovery projects. Currently,
hits as starting points for medicinal chemistry optimizations
are mostly found by high-throughput screening (HTS)
campaigns and to a much lesser extent by structure-based
approaches including fragment-based and computational
drug discovery. For certain target classes, however, HTS
often yields very low numbers of hits.[1] For example, protein–
protein interactions (PPIs) are notoriously difficult to hit with
druglike small molecules.[2] This has been assigned to the
unusual structure, topology, and flexibility of protein–protein
interfaces.[3] The fact that several drugs targeting PPIs have
recently entered the clinical development clearly shows that
certain PPIs, for example, between Bcl-x and XIAP, can be
efficiently targeted by small molecules.[4] Herein, we describe
a complementary process that led to the parallel discovery of
several compounds belonging to seven different scaffold
classes, amenable to synthesis by efficient multicomponent
reaction (MCR) chemistry in just one step, which antagonize
the PPI between the transcription factor p53 and its negative
regulator Hdm2.
Protein–protein interactions are often mediated by only a
few key amino acid side chains and the terms “hot spot” and
“anchor” have been introduced for such locally constrained
areas and amino acids on the surface of interacting pro-
teins.[2,5,8] In a first approximation, the depth into which a
specific amino acid side chain of the donor protein is buried in
the acceptor protein is indicative of its energetic importance.
We reasoned that this “anchor” amino acid side chain might
serve as a reasonable starting point for the design of
(ant)agonists of a PPI. Thus, we use this particular amino
acid side chain as an initial anchor in virtual libraries of low-
molecular-weight scaffolds. Virtual compounds containing
anchor side chains are selected for synthesis and screening
based on their docking into the PPI interface. The starting
point for the docking/energy minimization procedure is
chosen in such a way that an overlap between the anchor
and the template amino acid side chain is ensured. In order to
rapidly test these ideas, we chose an efficient and fast but
versatile synthetic approach, MCR (Figure 1).[6] MCR allows
for the assembly of many diverse and complex scaffolds in a
one-step/one-pot manner, thus saving time and resources, and
potentially increasing the success rate of lead discovery.
The PPI interface of p53/Hdm2 has been characterized in
molecular detail by X-ray structure analysis.[7] It relies on the
steric complementarity between the Hdm2 cleft and the
hydrophobic face of the p53 a-helix and, in particular, on a
triad of p53 amino acids Phe19, Trp23, and Leu26, which
insert deep into the Hdm2 cleft (Figure 1A in the Supporting
Information). We chose the indole side chain of Trp23 as the
anchor residue for three reasons: 1) it is the central amino
acid of the triad, thus facilitating addressing by the antago-
nists the crucial Phe19 and Leu26 binding sites; 2) it is deeply
buried in Hdm2; and 3) it also features, in addition to
extensive van der Waals contacts, a hydrogen bond to the
Leu54 backbone carbonyl oxygen of Hdm2. In fact, calcu-
lation of the solvent-accessible surface areas of all amino
acids in the p53/Hdm2 interaction ranks Trp23 the highest
(Trp23 > Phe19 > Leu26).[8] Next, from our in-house database
of several hundred MCR scaffolds, we selected forty MCR
scaffolds to create virtual compound libraries.[6] By design,
each of the compounds incorporated the anchor. We used
indole and bioistosteric 4-chlorophenyl derivatives[24] sup-
plied with the corresponding functional groups as anchors to
[*] Dr. B. Beck, Dr. S. Srivastava, Y. Huang, Prof. A. Dꢀmling
Departments of Pharmaceutical Sciences and Chemistry
University of Pittsburgh, Biomedical Science Tower 3
3501 Fifth Avenue, Pittsburgh, PA 15261 (USA)
Fax: (+1)412-383-5298
E-mail: asd30@pitt.edu
Dr. A. Czarna, G. M. Popowicz, S. Wolf, M. Bista, Prof. T. A. Holak
Max-Planck-Institut fꢁr Biochemie, Martinsried (Germany)
[**] MCR: multicomponent reaction. We thank Dr. Ulli Rothweiler for
fruitful discussion. This work was supported by the NIH (grant
1R21M087617-01 to A.D.) and the Deutsche Krebshilfe (grant
108354 to T.H.) and is part of an NCI-RAND program. We thank
Haixia Liu for the synthesis of PB3.
Supporting information for this article is available on the WWW
5352
ꢀ 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Angew. Chem. Int. Ed. 2010, 49, 5352 –5356