个人简介

B.Sc. (Fudan University), 2003; Ph.D. (HK), 2008

研究领域

Chemical biology and biochemistry, Organic chemistry, Analytical Chemistry

Develop chemical approaches to i) identify and examine protein post-translational modifications (PTMs); ii) identify and perturb protein-protein and small molecule-protein interactions. Research programmes: Identify protein-protein 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 ('readerss') 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 to identify 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 protein can 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.

近期论文

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Li, X. and X. D. Li* (2014). Chemical proteomics approaches to examine novel histone posttranslational modifications. Curr Opin Chem Biol 24C: 80-90. Bao, X. Wang, Y. Li, X. Li, X. M. Liu, Z. Yang, T. Wong, C. F. Zhang, J. Hao, Q. X. D. Li*. (2014). Identification of 'erasers' for lysine crotonylated histone marks using a chemical proteomics approach. Elife 3. X. Bao, Q. Zhao, T. Yang, Y. M. Fung*, X. D. Li*. A Chemical Probe for Lysine Malonylation. Angew Chem Int Ed. 2013, 52, 4883. B. Shen#, X. Li#, F. Wang, X. Yao*, D. Yang*. A synthetic chloride channel restores chloride conductance in human cystic fibrosis epithelial cells. PLoS One. 2012, 7, e34694. (#co-first author). 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*. Alpha-aminoxy acids: new possibilities from 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, 129, 7264. X. Li, D. Yang*. Peptides of aminoxy acids as foldamers. Chem. Commun. 2006, 3367. D. Yang*, X. Li, Y.-F. Fan, D.-W. Zhang. Enantioselective recognition of carboxylates: a receptor derived from alpha-aminoxy acids functions as a chiral shift reagent for carboxylic acids. J. Am. Chem. Soc. 2005, 127, 7996. D. Yang*, X. Li, Y. Sha, Y.-D. Wu. A cyclic hexapeptide comprising alternating -aminoxy acids and -amino acids is a selective chloride ion receptor. Chemistry-A European Journal. 2005, 11, 3005.