Tetrahedron Letters
Synthesis of isoprenoid chain-contained chemical probes for
an investigation of molecular interactions by using quartz crystal
microbalance
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Wujun Liu, Yixin Zhang, Shuhua Hou, Zongbao Kent Zhao
Division of Biotechnology and Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, CAS, Dalian 116023, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 29 June 2013
Revised 25 August 2013
Accepted 2 September 2013
Available online 10 September 2013
Five probes including four that contained isoprenoid chain were synthesized. These probes were assem-
bled onto the gold-coated quartz crystal chips for analysis of their interactions with four yeast proteins by
using the quartz crystal microbalance technology. Results showed that 3-phosphoglycerate phosphoki-
nase and triosephosphate isomerase had clear interactions with certain probes, while glutathione reduc-
tase and phosphoglucose isomerase gave much lower interaction signals. It also suggested that 3-
phosphoglycerate phosphokinase had two sites interacting with the probe attached with a geranyl moi-
ety. Further molecule simulation experiments provided supportive information on these intermolecular
interactions. Together, our data suggested that there are hydrophobic interactions, with relatively good
selectivity, between isoprenoid chain and proteins.
Keywords:
Isoprenoid chain
Chemical probe
Molecular interaction
Quartz crystal microbalance
Molecular docking
Ó 2013 Elsevier Ltd. All rights reserved.
Isoprenoid chains such as isopentenyl, geranyl, farnesyl, and
geranylgeranyl, are building blocks for many natural molecules,1
terpenoids, sterols, carotenoids, and dolichols.2 They are also pres-
ent as intact tails in ubiquitous biologically active molecules such
as vitamin K, coenzyme Q, tocotrienols, and flavonoids.3 Further-
more, they can be attached to a protein through a process called
protein post-translational modification.
Similar to long chain fatty acids interacting with their target pro-
teins,7 isoprenoid chain may also follow hydrophobic interactions
with proteins. In biology, hydrophobic interactions are the most
important non-bonded interactions which determine protein fold-
ing8 and ligand-receptor binding.9 While ionic interaction and
hydrogen bonding can be determined relatively easily according
to structural information, it is more difficult to use a quantitative
method to find the hydrophobic interaction site.10 Moreover,
hydrophobic interactions are expected to be much weaker than
other interactions, which furnish intrinsic difficulty for detection
and quantification. Both surface plasmon resonance11 and quartz
crystal microbalance (QCM)12 are surface-sensitive, label-free tech-
niques for real-time monitoring of small mass changes to reveal
useful information about the binding event, for which they have
been widely used in analysis of molecular interactions involving
small organic molecule,11,13 biomolecules,14 DNA,15 and peptides.16
Although the benzophenone moiety could partially mimic iso-
prenoid chain, benzophenone-based compounds were weak com-
petitive inhibitors to PPTases,17 suggesting that the structure of
probe should be redesigned. In this Letter, we reported our results
on the synthesis of five new probes (Scheme 1) and their interac-
tions with four yeast proteins by using the QCM technology. Fur-
ther molecule simulation experiments provided supportive
information on these molecular interactions. Our data suggested
that there are hydrophobic interactions, with relatively good selec-
tivity, between isoprenoid chain and proteins.
The isoprenoid chain per se may have interactions with different
acceptors in the biological systems, such that the presence of the
isoprenoid chain concerned many processes, for example, natural
product biosynthesis and some metabolic diseases.4 However,
these interactions have been poorly documented; partially because
the isoprenoid chain is chemically unreactive in the intracellular
environment. In an early study, we prepared photoaffinity probes
that contained the biotinyl group and benzophenonyl moiety
linked to the terminal carbon of the geranyl group, and performed
a chemical proteomic analysis of the interactions between those
probes and the proteome of the yeast Saccharomyces cerevisiae.5
There were 30 proteins with a variety of biological functions being
identified. These proteins could be classified as a kinase, ATP
related enzyme, dehydrogenase, and endonuclease. To improve
the efficacy of the synthetic probe for discovering and profiling
the elusive isoprenoid chain interactome, we also synthesized a
number of structurally different probes and demonstrated their
capability in terms of capturing proteins from the yeast proteome.6
Probes 4a–4d and 6 were designed, which contained a lipoic
acid moiety as the anchor for assembling the probe on the gold-
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Corresponding author. Tel./fax: +86 041 84379211.
0040-4039/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.