公共头尾

XUE Min
Associate Professor, Department of Chemistry, University of California, Riverside

Brief bio: Xue Min graduated from Nanjing University with a B.S. in Chemistry. He obtained his Ph.D. in Chemistry from UCLA under the guidance of Prof. Jeffrey Zink, working on supramolecular drug delivery systems and excited-state mixed-valence analysis. He then conducted postdoctoral research at Caltech in Prof. Jim Heath's group, switching to the fields of single-cell analysis and systems biology. In 2016, he started his independent career in the Department of Chemistry at UC Riverside and was promoted to Associate Professor with tenure in 2022. His current research focuses on developing molecular tools for biomedical applications. His work is recognized by the NIBIB Trailblazer Award, the NIGMS MIRA, and the DoD Career Development Award.

Topic: Accessing the 3D-Diversifiable Chemical Space With in Situ Click Strategies

Abstract: Molecular probes capable of specific recognition of protein epitopes are the basis of many chemical biology studies. De novo discovery of such probes often requires screening of chemical libraries, which also prevails in current drug development pipelines. Because a larger library capacity promises a higher probability of identifying hits, methods to increase chemical diversity are highly desirable. Accessing spatial diversity, i.e., manipulating the spatial arrangement of functional groups, represents a more effective tactic to expand chemical diversity than changing functional groups and building blocks. This benefit is especially prominent when the molecular structures exhibit true 3D topologies, as opposed to the 2D scaffolds often observed in traditional small-molecule libraries. Here, we showcase a few examples of cyclic peptide libraries providing access to unique 3D-diversifiable chemical space. When coupled with in situ click approach, these libraries can generate chemical probes for challenging protein targets, such as MMP2 and MYC. We demonstrate that these probes can enable unique therapeutic opportunities.

SHUI Wenqing
Associate Professor, iHuman Institute, School of Life Science & Technology, ShanghaiTech University

Brief bio: Dr. Shui Wenqing is leading a research group of G protein-coupled receptor (GPCR) Omics & Ligand Discovery. The main research interest of Shui Group is to develop high-throughput affinity MS techniques for the discovery of GPCR ligands with new chemical scaffolds and unique pharmacological properties. This affinity MS-based platform, when combined with omics technology or modular click chemistry, enables the discovery of a variety of new GPCR modulators from either synthetic libraries or natural herb extracts. Meanwhile, Shui Group has established experimental and bioinformatics approaches for in-depth transmembrane proteome profiling to facilitate potential drug target discovery from the GPCR superfamily.

Topic: GLP-1 Receptor: What Can We Do After Solving Its Structures?

Abstract: GLP-1 receptor (GLP-1R) is a prototypical class B G protein-coupled receptor which is predominantly coupled to the stimulatory G protein Gs to mediate intracellular signaling. Multiple peptide agonists that activate GLP-1R are approved, or in clinical development, for the treatment of type 2 diabetes and/or obesity. Apart from peptide-based drugs, the identification of small molecules to activate the GLP-1R has aroused wide interest. We developed a new platform for the design, synthesis, and screening of customized triazole libraries. By integrating double-click chemistry and affinity-selection mass spectrometry, we identified a series of positive allosteric modulators (PAMs) with unreported scaffolds that can selectively and robustly enhance the activity of the endogenous GLP-1(9-36) peptide. We further revealed an unexpected binding mode of the new PAM series to the receptor.

To promote mechanistic understanding and drug development, a number of high-resolution structures have been determined for the active-state GLP-1R-Gs complex bound to a peptide or a small-molecule agonist. By combining cross-linking mass spectrometry (CLMS) with integrative structure modeling, we map the conformational ensemble of the activated GLP-1R-Gs complex at near-atomic resolution. The integrative structures describe heterogeneous conformations for a high number of potential alternative active states of the GLP-1R-Gs complex. These structures show marked differences from the previously determined cryo-EM structure, especially at the receptor-Gs interface and in the interior of the Gs heterotrimer.

Finally, we have used the GLP-1R structure to guide our design of a proximity labeling probe for systematic mapping of the cell-surface protein interactome with GLP-1R. We have identified several unknown GLP-1R interacting partners that may vary in different cell types relevant to the receptor physiology.

Sara H. ROUHANIFARD
Assistant Professor, Bioengineering, Northeastern University

Brief bio: Prof. Rouhanifard received her B.S. in Biochemistry and Molecular Biology from UMass Amherst in 2007. She then completed a Ph.D. in Biochemistry at the Albert Einstein College of Medicine under the supervision of Wu Peng, developing chemical tools to probe glycosylation in cells using biorthogonal chemistry. She then joined the laboratory of Arjun Raj Bioengineering department at the University of Pennsylvania as a postdoctoral associate and a NIH Ruth S. Kirschstein F32 National Research Service Award fellow, where she developed single-molecule approaches to image RNA in cells. She joined the Northeastern Bioengineering department as an Assistant Professor in 2019. Her primary research interests lie in understanding the epitranscriptome and related mechanisms that govern cellular differentiation and response to external stimuli. The Rouhanifard laboratory develops quantitative, single-molecule sequencing and imaging approaches using new chemistry to identify and perturb sites of RNA modifications to reveal specific biological functions that may be exploited for the development of future therapeutics.

Topic: DNA-Enhanced CuAAC Ligand Enables Live-Cell Detection of Intracellular Biomolecules

Abstract: Of the various conjugation strategies for cellular biomolecules, Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is the preferred click chemistry approach due to its fast reaction rate and the commercial availability of a wide range of conjugates. While extracellular labeling of biomolecules using CuAAC has been widely adopted, intracellular labeling in live cells has been challenging; the high copper concentration required for CuAAC reaction can be toxic to biological systems. As a critical first step towards achieving intracellular labeling with CuAAC, an ultrasensitive CuAAC ligand is needed to reduce the required copper concentration while maintaining fast reaction kinetics.

We have developed a new, DNA oligomer-conjugated CuAAC accelerating ligand BTT-DNA for biomolecular labeling. The DNA oligo attachment serves several purposes: 1. Increases availability of local copper atoms in proximity to the ligand, thus enabling the ligation of azide tags with much lower copper concentrations as compared to commercially available CuAAC ligands, and 2. Allows nucleic acid template-driven proximity ligation through the choice of the attached DNA sequence. We show that BTT-DNA significantly enhances CuAAC reaction kinetics in vitro and can achieve intracellular labeling of alkyne-tagged biomolecules in vivo. We also demonstrate that this reaction may be used as a proximity ligation using intracellular target RNA or DNA. This new ligand advances our efforts toward the final goal of applying CuAAC for intracellular, live-cell applications.

WANG Lei
Professor, Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco

Brief bio: Prof. Wang Lei received BS and MS from Peking University, and PhD from UC Berkeley mentored by Peter G. Schultz. His graduate research resulted in the first expansion of the genetic code to include unnatural amino acids (Uaas) in 2001, for which he was awarded the Young Scientist Award by the Science magazine. After postdoctoral training with Roger Y. Tsien (Nobel Laureate in Chemistry), Wang started his group at the Salk Institute in 2005 and moved to University of California San Francisco in 2014. His group has developed new methods for the expansion of the genetic code in a variety of cells and animals. Wang discovered that release factor one is nonessential in E. coli, and engineered autonomous bacteria capable of incorporating Uaas at multiple sites with high efficiency. Recently, Wang pioneered the concept of proximity-enabled bioreactivity and demonstrated the genetic encoding of latent bioreactive Uaas in live systems. This new class of Uaas enables bioreactivities, inaccessible to proteins before, to be specifically introduced into biosystems, opening the door to harnessing covalent chemistry for protein engineering and biological research in vivo. Wang is a Top Young Innovator (by MIT Technology Review), a Basil O'Connor Starter Scholar, a Beckman Young Investigator, a Searle Scholar, an NIH Director's New Innovator Awardee, and a recipient of the Emil Thomas Kaiser Award.

Topic: New Covalent Bonding Ability for Proteins

Abstract: To genetically introduce new chemical reactivity into live systems, we engineered the genetic code to encode a new class of unnatural amino acids (Uaas), the latent bioreactive Uaas. These Uaas, after being incorporated into proteins, specifically react with target biomolecules via proximity-enabled reactivity, enabling the selective formation of new covalent linkages between proteins and biomolecules in vitro and in live systems. These diverse reactivities, inaccessible to natural proteins, open new avenues for protein engineering, biological research, and therapeutic applications. Latent bioreactive Uaas bearing functional groups capable of Sulfur-fluoride exchange (SuFEx) reactions have been found highly efficient and biocompatible. We harnessed the genetically encoded, proximity-enabled SuFEx reactivity to probe protein-RNA interactions, to irreversibly crosslink carbohydrates with proteins, and to develop covalent protein drugs.

Reversible RNA methylation in gene expression regulation

Prof. Chuan He

Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago

Over 150 types of post-transcriptional RNA modifications have been identified in all kingdoms of life. We have discovered two RNA demethylases, FTO and ALKBH5, which catalyze oxidative demethylation of the most prevalent modifications of mammalian messenger RNA (mRNA) and other nuclear RNA, N6-methyladenosine (m⁶A). These findings indicate that reversible RNA modification could impact biological regulation analogous to the well-known reversible DNA and histone chemical modifications. We have also characterized proteins that selectively recognize m⁶A-modified mRNA and affect the translation status and lifetime of the target mRNA. Functional studies reveal m⁶A methylation as a critical mechanism to group transcripts for coordinated metabolism, translation, and decay, allowing timely and coordinated protein synthesis and transcriptome switching during cell differentiation and development. I will present our recent work elucidating transcriptional regulation through m⁶A methylation and demethylation, and impacts of this regulation on mammalian early development as well as plant growth.

Lnc-ing RNA processing and function

Prof. Ling-Ling Chen

New Cornerstone Science Laboratory, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences (CAS)

Long noncoding RNAs (lncRNAs) are emerging as new regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Many lncRNAs are transcribed by RNA polymerase II and are capped, polyadenylated, and spliced like mRNAs. By developing methods for genome-wide discovery and characterization of non-polyadenylated RNAs, we have identified several RNA species with unexpected formats. These RNAs are derived from long primary transcripts via unusual RNA processing pathways and are stabilized by distinct mechanisms, including capping by small nucleolar RNA (snoRNA)–protein (snoRNP) complexes at their ends (sno-lncRNAs) or forming circular structures. We have shown that sno-lncRNAs and circular RNAs are involved in key gene regulation events and are implicated in Pradier-Will syndrome and autoimmune diseases. In this talk, I will discuss the mechanisms of their formation and function, as well as how we study one sno-lncRNA (SLERT) that has enabled us to uncover previously unknown organization and regulation in the human nucleolus.

Translating spatial cell atlas to tissue function

Prof. Xiao Wang

Department of Chemistry, Broad Institute, MIT

Spatially charting molecular cell types at single-cell resolution across the entire three-dimensional (3D) volume of the brain is critical to illustrating the molecular basis of the tissue anatomy and functions. Recent development of spatial transcriptomic methods has enabled scalable profiling of transcriptome-defined spatial cell atlas. Yet, there is still a big gap between spatial cell atlas and tissue function. In this presentation, I will introduce a few experimental and computational advances in our lab that further enable multi-modality deep profiling of cell types and states in situ, bridging single-cell molecular profiles with single-cell functional status in intact biological tissues and accelerating gene-to-function discoveries in development and diseases.