Research in our group aims at developing chemical approaches
to identify and perturb protein-protein and small molecule-protein interactions.
interactions mediated by posttranslational modifications (PTMs)
Post-translational modifications (PTMs)
such as acetylation, methylation, and phosphorylation play crucial roles in regulating the
protein-protein interactions that are involved in essentially every cellular process.
While significant progress has been made to detect PTMs, identifying protein-protein
interactions mediated by these PTMs remains a challenge.To develop a robust method to
analyze PTM-dependent protein-protein interactions, we focused on histones. These
widely conserved proteins assemble into nucleosomes, around which DNA is packaged
to form chromatin.Numerous PTMs, such as methylation, phosphorylation, acetylation
and ubiquitylation, have been found on histones. These histone PTMs can serve as a
signaling platform that would be recognized (or 'read') by specific binding proteins,
which would then, in turn, regulate DNA-templated processes, such as gene transcription,
DNA replication and DNA damage repair.While various PTMs have been detected at more than
70 different sites of histones, the progress on finding proteins that recognize these PTMs
have largely lagged behind. To fill this knowledge gap,we have developed a chemical
proteomics approach that combines a photo-cross-linking strategy with state-of-the-art mass spectrometry
to identify PTM-dependent protein-protein interactions.
Perturb histone PTM-dependent
protein-protein interactions by developing peptidomimetic inhibitors
Histone PTMs (e.g. acetylation,
methylation and phosphorylation) play important roles in many essential cellular processes
such as gene transcription and DNA damage repair. Misregulation of histone PTMs has been
implicated in human diseases such as cancer and developmental abnormalities. Proteins
involved in regulating histone PTMs have therefore become potential drug targets.
Successful efforts have been made on targeting histone modifying enzymes that
generate ('write') or remove ('erase') PTMs on histones. However, the development
of potent chemical inhibitors that perturb interactions between histones and their
binding proteins ('readers') has largely lagged behind. As peptide-based inhibitors,
which have large interacting surfaces, provide the prospect of enhanced potency and high
specificity for the inhibition of protein-protein interactions, we are using a peptidomimetic strategy to develop
specific inhibitors that target 'readers' of histone PTMs.
Identify protein targets of small
molecules (i.e., drug target I.D.) by chemical proteomics
Small molecules have
been widely used as not only valuable tools to elucidate complex networks of cellular
processes but also important therapeutic agents to treat human diseases. Most
small-molecule probes and drugs interact with more than one protein targets in
the cell, and thereby, they usually exert complex effects on multiple cellular
pathways.A complete understanding of a small molecule's interacting partners,
including its 'on-target' and 'off-target' proteins, remains extremely rare. To this
end, we are developing a quantitative mass spectrometry-based affinity chromatography
approach toidentify proteome-wide small molecule-protein interactions. We are going to
apply this chemical
proteomics approach to comprehensively identify protein targets of anticancer drugs.
Map small molecule-protein binding sites
Understanding of how
a bioactive small molecule interacts with its target proteincan provide important
information for improving potency and specificity of the molecule.However, in many
cases, a co-crystal structure of the small molecule bound to its target protein is
difficult to obtain. To map a small molecule's binding site in its target, we have
developed a method using Stable Isotope Labeled Inhibitors for Crosslinking (SILIC).
In SILIC, an equimolar mixture of small-molecule analogs that incorporate a
photo-cross-linking group along with natural and 'heavy' isotopes, respectively,
are used to capture the target proteins and generate a robust signature for
identifying small molecule-modified peptide fragments in complex mass
spectrometry data. In future studies, we will combine our chemical proteomics
approach (see above) and this SILIC method to not only identify targets of
anticancer drug molecules but also analyze the drug-protein binding modes,
which would advance our understanding of existing drugs,
as well as guide the further design of new therapeutic agents.
- X. Li,
E. A. Foley, K. R. Molloy, Y. Li, B. T. Chait, T. M. Kapoor*,
Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions.
J. Am. Chem. Soc.,2012, 134, 1982.
- X. Li, T. M. Kapoor*,
An optical switch for a motor protein.
ChemBioChem, 2011, 12, 2265.
- S. A. Wacker, S. Kashyap, X. Li*, T. M. Kapoor*,
Examining the mechanism of action of a kinesin inhibitor using stable isotope labeled inhibitors for cross-linking (SILIC).
J. Am. Chem. Soc., 2011, 133, 12386.
- X. Li,T. M. Kapoor*, Approach to profile proteins that
recognize post-translationally modified histone "tails".
J. Am. Chem. Soc., 2010, 132, 2504.
- X. Li, B. Shen, X.-Q. Yao, D. Yang*,
A synthetic chloride channel regulates cell membrane potentials and natural voltage-gated calcium channels.
J. Am. Chem. Soc. 2009, 131, 13676.
- X. Li, Y.-D. Wu*, D. Yang*, α-Aminoxy Acids: From New Foldamers to
Anion Receptors and Channels. Acc. Chem. Res. 2008, 41, 1428.
- X. Li, B. Shen, X.-Q. Yao, D. Yang*,
A small synthetic molecule forms chloride
channels to mediate chloride transport across cell membranes. J. Am. Chem. Soc. 2007,
X. Li, D. Yang*, Peptides of aminoxyacids as foldamers. Chem. Commun. 2006, 3367.
D. Yang*, X. Li, Y.-F. Fan, D.-W. Zhang, Anenantioselective carboxylate
receptor derived from α-aminoxy acids functions as a chiral shift reagent.
J. Am. Chem. Soc. 2005, 127, 7996.
D. Yang*, X. Li, Y. Sha, Y.-D. Wu, A cyclic hexapeptide comprising
alternating α-aminoxy acids and α-amino
acids is a selective chloride ion receptor. Chemistry - A European Journal.
2005, 11, 3005.